The trolling motor (24V) system needs to be dedicated with nothing else running on it. Those batteries should be group 27 or larger, I recommend group 31 if you like to fight elements or troll with your bow mount.
As mentioned, use 6 awg wire up to bow mount from where batteries are located. The negative terminal of starting (12V) should be tied to negative terminal of 24v system (make sure you pick terminal not in series with positive terminal of other battery). This connection will eliminate noise.
Try to make sure you do not run your ethernet/link cable in the same runs as power cables. You should also try and run 12v and 24v power cables away from each other as well to eliminate noise sources.
The trolling motor I believe has a ground lead to connect to bow mount locator, make sure you make this. I had to add it ex-factory on my bird to eliminate noise but I believe it is now on units standard.
You should heat shrink power connections to prevent corrosion. Make sure you put a self resetting breaker with APPROPRIATE rating on the positive terminal of 24V system. A relay breaker on motor alone is not enough because nothing is protecting 6awg wire running to motor.
I would also recommend a 3 bank on board charger as part of upgrade to maintain all batteries when boat is not in use.