I'd go with three batteries.

One deep cycle for the trolling motor. Make that a stand-alone circuit.
If you're going to troll for long periods, make sure you have plenty of
amphours. If you can avoid discharging the battery to less than 50% of
capacity, even a deep cycle, it will provide longer and more reliable
service.

A dedicated starting battery for your electric start. Don't put
anything else on this circuit, (IMO), it's just too important to share
with less critical applications like horns, aerators, etc.

A deep cycle battery for the aerator, nav lights, bilge pump, etc.

Connect the starting battery and accessory deep cycle batteries through
a make before break selector switch, ("1,2, both, off"). That will
allow you to draw some juice from the accessory battery, if needed,
when starting your motor.

That may sound like a lot of batteries, but you don't want to go
cheapie with your electrical system. The batteries may not need to be
all that big- and in a 17-footer you don't want to use extra space for
anything, but what should be a two battery setup becomes three with the
trolling motor.