I guess that i've found "inner peace" in the matter by not thinking or worrying about it! My solar panels stay "on" all of the time, even when connected and towing. When I get where I'm going, my batteries always read fully charged. I don't know if that charge comes from the solar or from the truck-pin supply, or from a combination, but either way it's full. I've had no proplems with the truck's charging or electrical system, as a result of being conected to the TT with the solar array "on".
2014 RAM 2500 Laramie 4x4 Quad Cab w/Cummins Turbo Diesel, 2009 Rockwood 2607, and 3 'yaks!
300W of Suntech Solar, a Rogue MPT-3024 Controller, and a Xantrex PW2000 Inverter