Re: Will this dual battery setup do what I want it to?
To determine if this system will actually benefit you, we need to know what engine you have so we have some idea of the output of the alternator. Knowing what thrust the trolling motor has allows us to determine what the actual current draw is. Any alternator will provide a charge to a battery. How much output that alternator has and how discharged the battery is determines how long it takes to charge the battery. You can figure this out using the following example and applying it to your situation.
If the trolling motor is a 50 - 55# thurst unit it will draw about 45 amps maximum for each hour it is run. Since that number is rarely reached and since trollers aren't usually run at fastest speeds continuously, lets use a 23 amp/hr number which also happens to be the rating specification used on deep cycle batteries. Lets also assume you have a group 27 deep cycle battery which will have a reserve capacity of 175 minutes with a current draw of 23 amps. That means your troller would run for just shy of three hours before the battery could no longer deliver 23 amps. Lets also assume the alternator has a maximum output of 23 amps. That means you would have to run your engine wide open for the same period of time (and probably longer) to recharge the troller battery. Keep in mind the alternator also has to supply the other electrical needs of the boat so the recharge time will be much longer. So armed with those numbers you can do your own math to determine if this is a workable solution. I suggest it is not and the external battery charger and extension cord take up so little room and is much more practical.