You will get more runtime off a 24V trolling motor than a 12V with two batteries in parallel or switched.
the reason is the 24v will run at lower power vs 12V for same thrust.
I would never recommend anyone ever get a 12v trolling motor unless they really are not a serious fishermen.
Did that last fall and haven't had a chance to use it. Thats on a 19' ranger. Thinking I should have gone with an 80# now. Do lots of river fishing.
one thing recommended if wiring 2 12v batteries in parallel is to be sure both batteries are matched and in same condition... I think that may have more to do with charging, but recall reading that
edit: here's an example, but you can find out more by searching
from the article : "Try to match capacities as much as possible. When connecting batteries in a pack you should try to match the capacities as much as possible to avoid discharging one battery quicker than another. A pack operates at a combined voltage so your one cell that discharges quicker will likely discharge deeper than it may be able to recover from"
My brother runs his 12v off of two batteries with no issues at all. The only thing to consider is if the second battery will upset the weight distribution/balance of your boat. Stuffing two batteries just for a 12v trolling motor into a smaller boat can really throw you off.