Just to go overboard: here are a couple photos of the solar controller mounted:

Good luck with the install.

MC4's are fine to be disconnected and reconnected but to meet the National Electric Code all solar module connectors must require a tool for removal. That is a safety requirement so that people can't go wandering out in a solar array and disconnect the modules by hand and electrocute themselves with 600 or 1000Vdc. They are NOT approved for load break, meaning that you need to disconnect the solar module/array somewhere else first so that there is no current flow when you disconnect the modules. Solar is always on when the sun is shining so there has to be another way to disconnect the module(s), otherwise you will draw an arc. Its not a big issue at 12Vdc but at 600Vdc I can assure you that it gets pretty interesting.

Offgrid recommendations are right on. I'm only going to add some detail from the installation of the solar controller on my 172:

When I exposed my wiring by removing the little knock out panel in my upper cabinet behind the solar sticker, I could see the two 10 Ga wires (mine were brown and yellow) coming out of the roof, coiled inside the cabinet, and exiting back into the ceiling near the center of the camper (on it's way to the battery):

The bottom of the MC-4 port on the roof was visible from the inside of the cabinet, as were the wire nut connections from the port (red and black) to the trailer wiring (brown and yellow):

I tested the wires and MC-4 port, marked positive and negative (I could also locate the yellow and brown wires where they tied to the battery), disconnected the battery, tested them again... repeated that again because I wanted to be 100% sure... and finally cut the wiring in the cabinet. 

I connected the wires from the roof port (without the panel connected) into the correct terminals on the controller, did the same with the battery side, hooked everything else up and had a bit of a tantrum because the controller wasn't in "charge" mode. It took me about an hour and a half of being an idiot to find out I had a bad MC-4 connector and when I replaced it, everything worked great.

Good luck. 

Click on the little tree icon an it will walk you though attaching a pic. Its a 2 step process. upload then attach. Also don't attach too big a photo, reduce the resolution first. 

Re the electrical connection, I believe that the continuous loops of wire go from the roof to the battery and you are expected to cut them to add in the controller. But, to be sure, if you don;t have a multimeter, get one. Use it to confirm where the wires go.

 To do that first see if the there are two wires at the battery that look to be the same as the ones behind the label and on the roof. If there are then disconnect them from the battery, use the dc V scale on your meter, and confirm there is no voltage between them. If there isn't then use the ohms scale to see what the resistance is between them. Should be showing an open circuit (very high or infinite resistance). Then, short them together. Then go on the roof, confirm there is no voltage between the two wires and confirm zero (or very low) resistance. Then you can short those together on the roof. 

Then you can safely cut the two wires behind the label, strip them, and confirm zero (or low) resistance on each of the two pairs. If you're not sure which pair goes to the battery and which to the roof, disconnect one set and check the resistance with your meter again. At that point you will know for certain which wires go where so you can disconnect the two wires from each other at the battery and roof and complete connections to your controller, solar module, and battery, being cautious to get the polarities right. 

Add an inline fuse at the + battery terminal if there isn't already one there. If the wires are 10 gauge you can use a 30A fuse, 20A for 12 gauge wire.

We are looking to do a roof mounted flexible panel as well. I'm curious to know what adhesive you used and if you had any insight or advice you'd be willing to share?

Thanks.

The Renogy system is easy, seems to be well built and is in a very durable storage case. We have used it for 3 years and are happy. Vann

+1 We have not used ours much outside of testing as our camping plans got changed by the current situation. However, it looks like camping in NC is opening back up so I hope we can do so soon. Instead of 2 6V batteries, I now have a single 100A LiFePO4 battery. In my testing, the panel worked quite well. If we do not have shore power, we use propane for those things that need it, to include hot water. I installed a couple of 12V outlets and a couple of USB outlets in our 2016 RP179. I use one of them for my CPAP machine. One USB outlet is used to charge our phones at night. The other 12V and USB outlets (actually, a triple-outlet with two 12V and one USB outlet) gets used for a 12V fan to help circulate air, especially if we don't have shore power and are not running the AC and other miscellaneous uses. I do have a small 100w inverter that is used periodically to run the television (cheaper than buying a 12V TV) and a 350w that rarely gets used. Most often, that is used in the truck to charge laptops while we are driving.

I also installed a Renogy RNG-DCC1212-20 DC to DC charger for the LiFePO4 battery that is able to supply much more power than the Frontier could through the stock 12V supply. I will be able to use that if sunlight is inadequate to charge the battery if shore power is not available also. In addition, if I want to be able to run the AC or the microwave, I do have a generator, but we don't need to use the microwave and if the weather is moderate, can skip the AC also which means we can leave the generator home and save the weight.

We also use a 100w Renogy suitcase set and love it.  We have about 35" of wiring that lets us pu th the panels in the sun.  It keeps our 2 6v GC batteries usable for days on end. We are frugal power users that mostly boondock. We don't use the water heater or the AC. We use solar lights (Luci brand) and heat water on the stove, refrig is always on propane. We do have a 750w inverter for charging electronics.

The Renogy system is easy, seems to be well built and is in a very durable storage case. We have used it for 3 years and are happy.

Vann

80 amp hours of LI battery is good for most folks.  It should provide enough current to run the microwave but you would need to buy a 2KW or larger sine wave inverter. Like this for example:

It will draw something like 150 amps from the battery running the micro so you will want to locate the inverter as close to the battery as possible and run at least 1/0 gauge wire to it from the battery, which is big stuff. 

If the charge controller that came with your solar modules is not set up for Li battery charging you should consider very carefully before you use it. Again, lithium batteries can catch fire if overcharged. Proper wire sizing and fuse protection for all the system components is also critical for safety. 

Documentation? There are numerous online resources. For lithium batteries and batteries in general I would take a look at batteryuniversity.com.  That's probably a good place to start. 

Are the two 40AH batteries you got 12V or 6V?  If they are 12V then you will be connecting them in parallel and will have 80AH capacity. if 6V then they need to be connected in series so you will have 40AH capacity. 

40AH is small for most folks, even though you can use most of that capacity with Li batteries. You should still not use more than than about 80-85% if you want to get long life out of them. So that's about 35AH in practice. 

All Li batteries are "smart" in that they need a battery management system (BMS) to be operated safely. So, be careful to really understand what protections the BMS your batteries have provides. If you overcharge Li batteries they can catch fire. The WFCO charger in your rPod left to its own can overcharge them. WFCO and others make different chargers meant for use with Li batteries. 

The other consideration besides overcharging is excessive discharging. Lead acid batteries can run as high as 14.4 V charging and as low as 11-11.5 V discharging. Li batteries have a much narrower voltage range, so if you have a Li battery that charges up to 14V it will be fully discharged around 12.5-13V. In other words, you don't want to discharge a Li battery to as low a voltage as you would a lead acid one. A battery monitor will help you to track your battery state of charge. They are available pretty inexpensively these days. 

Re inverters, no you don't really need one. You can't run your a/c on battery anyway, it takes waaay to much energy. That leaves your microwave and TV as the ac loads in the trailer as it comes from the factory. You can get a dual voltage TV pretty inexpensively, so that can be run efficiently on 12V. The microwave can in theory be run for short periods (a few minutes at most) from an inverter, but you'd need at least a 2kw inverter for that and a 40AH battery probably can't produce enough current to run it. So if you do without your microwave while boondocking you won't need an inverter unless you add some other ac loads to the trailer.     

No schematic but as GlueGuy says the circuits are pretty simple. Assuming by "two harnesses" you mean the 4 wires connected to the tongue mounted battery, one pair of these should go to the solar connector on the side of the trailer, the other pair (the ones with voltage on them) to the ac charger and dc fuse panel. 

You do not need to use the existing wires going to the solar connector. Many folks find it more convenient to run their own conductors from their batteries to their charge controller and on to their solar modules. Either way, please DO install a fuse or circuit breaker at the battery, it is unsafe to run an unprotected circuit from the battery, if you get a short you can burn up your trailer. 

Use at least 10 gauge wire and a 30A fuse. If you plan to keep your solar modules portable and run a longer set of conductors to them (over about 20 feet one way) then go to 8 gauge wire to keep your voltage losses down. 

You will need a solar charge controller configured for lithium batteries and should change out your ac charger as well, lithium batteries need a different charge protocol than lead acid batts. Also, you should not attempt to charge lithium batteries when they are below freezing, so many folks relocate them to the inside of their trailers from the tongue so they stay warm. 

When you say you want to extend beyond the 40 amp capacity of the batteries you have, I think you probably mean 40 amp hours. Amp hours are a measure of battery capacity. Amps are a measure of instantaneous power from the battery (assuming a nominal 12V battery).

 If you add 200 watts of solar to your system that will produce around 12-13 amps at full sun as GlueGuy says. Over a typical 4-5 hours full sun on a decent day you would get around 50 amp hours, more than what your battery can take even if you start with it fully discharged. What I'm leading up to is that 200 watts is really too much for a 40 amp hour battery. I would suggest staying with about 100 watts of solar and consider getting more battery capacity first before adding more solar (assuming you need more).