Thanks a lot for your response. I figured out a bit more by myself too in the meantime.
The wires with the little loops are linked to the main car battery, the chassis battery, just did a test, you were right on that. So for now I can just connect the charge controller to that battery (same way you did if I understood right) because it is also indirectly connected to the auxiliary battery anyway. Now I'm wondering typically are the batteries of an RV connected in parallel or series? I'm guessing they would be in parallel to keep the system at 12V.
Those two batteries came with the RV and are both under the hood and there is a "battery disconnect" switch on the dashboard that connects or disconnects them.
Also about the other wires that used to pump AC power from the generator into the transfer switch, I agree, this seems like a more risky operation. If anyone has a better knowledge about that I'd be happy to hear. Otherwise I could connect an inverter in between the charge controller and the transfer switch. The reason I want to be able to use the transfer switch is that it is connected to a series of AC outlets in the RV.
