I have always used deep cycle batteries because they are made to put out amps over a long period of time, unlike a car battery that has to put out a lot of cranking amps for short periods of time. I have no experience with gel batteries, but they are more expensive. I would just run the batteries separately, because it is best to drain deep cycle batteries as low as you can before recharging. Apparently, if you only discharge a new battery to half of its capacity a few times, it will develop a memory, and you won't get the full potential from it. Also, get yourself a deep cycle charger. I've had the best luck with the Energizer deep cycle batteries from Walmart - best bang for your buck!
If you run two of these in parallel, you could probably go all weekend if you are just trolling. I also check the water level in each cell before putting them on the charger, and add enough distilled water to cover the plates in each cell. This motor should have no problem pushing your canoe around.
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