Actually the voltage you have on your trolling motor doesn’t change how long you can run – that is determined by how much “juice” you have on board. Voltage (or pounds of thrust) has to do with how much power you have (e.g. can you hold in a 20 mph wind compared to a 30 mph wind).
To answer your question, in 95% of the situations you’ll face, a 24 volt trolling motor with at least 80 pounds of thrust is plenty of power. I do recommend however running 4 batteries to that motor (if your boat has the room) so that even if you have to run at 70% or 80% you can do so for a full day (8-9 hours).
If you choose to run a 36 volt motor, it too will last longer than a 2 battery 24 volt system – mainly because with the extra power, you will be running the motor at a lower speed – and you still have 3 batteries worth of juice.
Of course the other thing to consider is your batteries. Be sure you’re using quality marine batteries, and keep them charged between fishing trips, that way they’ll last longer and perform better for you trip after trip.