Ron is correct. "Overwiring" is just peace-of-mind and potential for expansion or improvemment. Choose as SHORT a route as possible. The mfgrs recommend the over the roof, down the vent, through the fridge compartment, etc route because it involves the least amount of drilling and sealing. For me, that would have required over 40' of wire run, or relocating my batteries to an inside (under dinette bench) location - a bad idea!
Check out my detailed install at VERY LONG - My 12V Electrical Modifications and Solar Power System Installation
. You will see that I ran my wires into a well sealed connenction box, then down through a closet to achieve the shortest possible run.
The wire from the panels should then run to a solar controller, matched to your panel outputs. There are a good variety of controllers out there, and after some research, I chose the Rogue, which I am VERY happy with! You then run out to the batteries, from there.
My factory converter is wired into the system, almost exactly the same as the way that it came from the factory. I just moved (shortened) the wires by 3' by bringing them inside to my junction box. This made the converter wire-run more effective (3'shorter - was 15% shorter) and it neatened-up my battery box (less cables and connections).
So think it out, just like you are doing. PLAN on going bigger, because once you see how effective it is, you'll want to take full advantage. Plan on a PSW (or similar) inverter to give yourself 120v on-demand..... if you plan on it, you'll wire for it, and you won't have to re-wire later.
You are learning about this exactly as I did... by researching and asking questions! It worked for me!!
Good luck with your project! Looking forward to seeing postings and photos!!!