I've tried figuring this out a few times but could never get a straight answer from anyone. It seems that my windlass, riggers and trap puller run off the start battery because they'll all kill it eventually. I sometimes end up having to hit that link foot switch thingy to get the port side started. There's a lot of confusion as to how it's all setup, or just a lack of caring by any shop to explain it because they're trying to deal with some other catastrophic failure that popped up out of nowhere and now they don't have time to deal with all the things that I actually wanted done. Classic.
So I just run both when using the windlass or puller.