Re: On-board charger question
Suggestion: Don't even consider one of the older 12/24 volt motors for a number of reasons. One is the very long description it takes to get electrically challenged folks up to speed and to get the blasted things wired properly. There are so many ways these things were wired that I won't even offer diagrams unless you first firm a plan. The motor is designed to deliver full power on 24 volts so why on earth they gave it 12 volt capability is a mystery (other than to allow one to poke alone on 12 volts -- but then thats why trollers have a speed control). If you have the choice of of 12 volts, 12/24, or 24, by all means, for simplicity, go EITHER 12 volts only or 24 volts only.
Lets cover some basics with parallel wiring. Unless you use an ACR/VSR or a dual battery switch, batteries wired directly in parallel will equalize -- meaning the weaker will always suck the life out of the stronger until the two are equal. If you use the boat frequently this is not an issue, nor is it a problem if both batteries are the same make, size, and age.
When you have just two batteries, one of which will be used for starting, then the above is even more important. The key is that you want to avoid having a dead starting battery which can very easily happen with batteries directly wired in parallel. With a switch, VSR, or ACR the batteries can be isolated so the dead starting battery issue is avoided. With a dual battery switch you can run everything off both batteries, or either of the two. You can also charge both batteries from the engine simultaneously or either one individually. The switch also allows you to actually start the engine off either battery or both. So that system is the least expensive, simplest and most versatile. That system is of course, a 12 volt only system. If you go 24 volts for the troller, you are again looking at three batteries. Two for the troller and a separate starting battery. Develop a plan and I will likely have a diagram for it.