Ive always been under the assumption parallel is always better. Creates longer amp hour draw time and by going in parallel it reduces heat or as much of a pull from say draw, ultimately giving you a little more time and efficiency. How much more time you get??? Depends on usage. Just make sure the batteries are setup as parallel and not in series. Seen that mistake made 1 too many times and next thing you know there is a 12v fried circuit board trolling motor collecting dust in someones garage.
BTW you may not be happy with your battery selection. According to their website, the max draw is 52 amps for this TM. This is directly from their website.
Trolling motors are measured in pounds of thrust, a static (unmoving) force, while gasoline powered engines are measured in horsepower, one HP is 550 ft-pound of work per second. Each is measuring different things, therefore they cannot be compared at face value. To estimate the horsepower of an electric motor, you need to know the watts used by the motor at its fastest speed. Most manufactures provide you with the amps a motor uses at full speed. We can convert this into watts by multiplying amps drawn with how many volts your battery produces (12V for one battery, 24 for two, etc.).
Example: The NV 55lb thrust motor draws 52 amps at full speed and uses one 12V battery.
(52 amps x 12V = 624 watts)
This gives us 624 watts.
Take the watts you calculated and divide it by 746 Watts (1 HP).
(624 watts / 746 watts = .83 HP)
So, our NV 55lb draws 624 watts at full speed, divided by 746 watts, gives us .83. Therefore, the estimated output of our NV 55lb is .83 horsepower.
I thought this was just an example to figure out HP on electric motor, so ill leave it up because its good info, but in the owner manual on page 4, the diagram shows this is in fact accurate.
ItemNo. Thrust(LBS) Thrust(KG) Input InputPower
NV-36 36 16.3 12V, 29A 348W
NV-46 46 20.9 12V, 40A 480W
NV-55 55 25.0 12V, 52A 624W
NV-62 62 28.2 12V, 58A 696W
NV-86 86 37.2 24V, 48A 1152W
If you are really on the TM and trying to get across the lake (since its your only means of propulsion) you will get max 2 hours out of both batteries... and thats pushing it. Run half power and you'll maybe get 4 hours of run time, but half the speed. See where im going with this? Anyways, hopes this helps.