Keep it simple - get a cranking marine battery for the main engine and dedicate it to do only that - you don't need to worry about a thing. Just like your car - put it in and enjoy your boat.
For the electric trolling motor get a dedicated battery for that and charge it up as needed - your boat won't be able to charge it enough with the amps it outputs anyways - so run it, and charge it. That is what a deep cycle marine battery is for.
It also completely eliminates the possibility of running your cranking battery down and getting stuck.
2 batteries - one cranking, one deep cycle. Done.
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