Let's understand this a bit better. Are you actually adding a second trolling motor battery (making a total three - two for the troller and one starting battery) or are you thinking about using the starting battery for the troller as well? Understand that if your current wiring is actually charging both batteries, that constitutes a parallel situation so they are not separate at all. But lets deal with your current situation (one troller & one starting battery). Those two batteries do not and should not have the negative terminals connected together, nor should the positives be connected whether they have fuses or breakers. I suspect you already have a 12 volt parallel system which means the weaker of the two batteries will suck the life out of the better battery whether or not you are using the troller. What you "say" you have is fine as long as the two batteries are not interconnected and only the starting battery will charge. You need to have a smart charger that you plug in at home or the dock to keep the troller battery charged as the engine simply cannot do that unless you run wide open for hours.. If there is a current path between both batteries you definitely have a 12 volt parallel system and no -- that is not a good system. It will work, but you run the risk of having a dead starting battery.
If you indeed plan to add a third battery (second troller battery) I would suggest a simple switch to connect and disconnect the two and again, keep those two 100% separate from the starting battery. The switch could be ON when using the troller, and OFF when not in use. You get very slightly longer run time that way.