First off, small outboards don't put out a lot of amps in the charging circuits. Of course, any is better than none, so I think you have a good idea. You could possibly use a dual battery switch. In #1 position you could have your cranking battery. In # 2 position, could be your troller battery. Once your main motor was started, you could switch to #2 position, and that should charge your troller battery. A word to the wise though. Be very careful what battery switch you buy. Some allow switching between batteries while running, and some don't. You should never switch to OFF while the motor is running or you could hurt the alternator. I think older battery switches moved to an off position while switching between #1 and #2. The newer ones won't do that, so your alternator will be okay. My newer battery switch states that is safe to switch between #1 and #2 on the run. Here's a Cabelas switch. Cabela's -- Perko Dual Battery Switch Personally, I would contact Perko and see you you can switch batteries on the run. The switch only states that you have to shut the engine down before switching to Off.