Not a dumb question at all. I don't run a trolling motor, but have have big boats with up to 3 batteries installed. I prefer BEP Marine battery switches as they have voltage sensing relays built in that charge any of the batteries (when the OB is running) whenever they need a charge. But they won't combine or go in parallel until you throw a switch to do so. Your OB could be on the Start battery switch and the trolling motor could go off the House position. If and only when you made need extra juice to start the motor would you combine them. See picture.
The problem with the simpler Off, 1, 2, Both switch you have is when set to Both ... you run the risk now having 2 bad batteries that won't start the motor. I've towed in or helped restart more than a few boats offshore that have had this happen. For example, if one was at 95% and the other at 35%, when set to Both - they will equalize, where the high one drains to the lower one, so you end up with two at 65%. I run big V6 OBs so I never want to be stuck with dead batteries, so I always have a 'hot' one in reserve.
What I do on my runs to the fish, is run #1 on the way out ... fish on whatever battery you need to, then start, switch to #2 and run back in on that one. I believe that helps equalize the charging back into your power if your OB charges your batteries.
But for your existing switch, Yandina also make a 'battery combiner' (also see picture) that essentially makes your switch work somewhat like the BEP Marine cluster, in that it only charges batteries (independently too) that may need it. But you still need to decide what battery you run off, where on the BEP you could be running both - OB and general loads off #1 and trolling motor off #1. They are kept separate or isolated from each other until YOU decide to join them.
But perhaps this is what you may want to add. And hopefully those who also run trolling motors in their setups can give you more direct experience.