My canoe days are way in the past, so my answer relies on dated experience.
From what I recall, weight was always a consideration with a canoe. For that reason, I'd be looking at a lithium (LiFePO4) battery. My 100AH lithium battery weighs 26 pounds. A comparable lead-acid battery would go much heavier.
If you can swing the cost, lithium is the way to go. There are budget lithiums; I have one. How much battery can you afford? I don't know that you need 100AH for a day trip in your canoe, but if you stay out overnight or a multi-day trip, then it might be important. I tend to go as big as I can with things like a battery.
The lighter lithium battery would make placement of the battery less critical. I think I would tend to put the battery in the center of the canoe to keep the canoe balanced fore and aft.
I'm not familiar with all of the battery box options.