I can't answer your switch question, as I only run a single battery. For checking the batteries, I would pull them out of the boat, charge them both, and then take them to a shop/store to have them tested-usually free. Then you have a solid answer to if the are good or not.
If they're the originals, I'm betting you need new
Batteries were bad. Went to an actual battery specialty store. Cranking one was completely shot, deep cycle was in the red. Only $195 for new ones, not too bad. I like specialty stores like that, they actually knew what they were talking about compared to autozone, and prices were better too.