Re: 12 volt or (2) 6 volt?
I just wanted to elaborate on the part about when to stop discharging your battery. Keep in mind using 12V should be fine, or any of the low voltage monitors they described! I'm just telling you how I'd do it to get maximum water time out of my battery without damaging it since a generic low voltage monitor isn't calibrated for my battery. Also the switch idea is great, because of the differences in batteries I'm about to explain. Silvertip's reasons for using the switch show how different batteries can be.
Most batteries have this drop-off point where they start losing voltage very fast (EVERY battery is different). When you find where this voltage point is for your batteries, then stop discharging them before this point and no damage should occur.
individually testing each battery would be best. You would then select the highest drop-off point of the two batteries and stop using the batteries before this voltage (See graph link below). To do this you can just keep measuring your voltage with a multimeter while you are using the trolling motor. You will see the voltage slowly lowering as time goes on, then at one point you will see it start going down fast.
Digital multi-meters use very little power since they put a high resistor in parallel with your circuit, so don't worry about it using too much power.
Here is a graph of different lead-acid batteries. Your battery will most likely be one of the higher C batteries.
http://www.powerstream.com/z/dh.jpg
The "C" rating means that the batteries maximum discarge is that many times the amp-hour rating. So if a battery is 1 amp-hour (Not amp/hour), with 20C, then it can continuously and safely discharge 20 Amps maximum for 1/20th of an hour. Likewise a battery of 1C which is 2 amp-hour can discharge at 2 amps for an hour (and no faster). If you can figure out your C rating, then you can see how your battery should perform among these guide lines. Notice that a 1C battery should discharge at full power in an hour (no less) but if you look at the graph, they discharge faster than that! Keep that in mind, as their maximum Amp-hour rating is higher than is acutally useable.
About my previous post, silvertip is right, series does not add the Amp-Hours, my mistake.
As for the other comments, it does get damaged by increase in internal resistance more during a full discharge and recharge (I've measured it after a fast recharge, I've done a lot of experiments on battery cells). As for the corrosion of plates, The plates are coated with a thin coat of lead sulfate when discharged. When recharged, it goes back to lead and sulfuric acid. However, if the battery remains discharged for a while that thin coat starts forming hard crystals of lead sulfate which can be nearly impossible to remove during a standard fixed voltage charge process. With the %'s you get, be careful using them because it is a percent of maximum capacity. How do you know where you are in capacity while boating? You'd need to characterize your battery (I have a table posted below which may help knowing % vs Voltage for the average battery).
Anyways, check the maintenance section here to see about the internal resistance
http://www.energymatters.com.au/renewable-energy/batteries/
The link below shows the drop-off Voltage in terms of %'s which may be helpful about 3/4's down the page. this page also says 20% is the minumum, but 50% is best for lifespan vs cost, which according to the table should happen around 12 Volts (so 12 volts should work), on most batteries.
http://www.windsun.com/Batteries/Battery_FAQ.htm#Cycles vs Life
Another page explaining how lead-acid internal resistance increases with discharge:
http://www.batteryuniversity.com/partone-22.htm
