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What Mako Mike said is right on, even for a smaller boat....A battery isolator isn't big or too costly and will charge the battery that needs charging regardless of position.
What Zacs said is true about switching while running. If the switch makes before breaks it is ok. But you really want to avoid this at all cost. I know my switch states not to. If contact points move and things don't make and break good then there is a chance of blowing your isolation diodes in your alternator that convert AC to DC since all induced current is alternating.
Personally unlike what Zacs said I always run on both batteries. There is nothing wrong with this while running. The batteries are always getting charged etc. If your engine is off and fishing using juice well that is another issue,... that is what I do. And I do not have a battery isolator yet but someday will install one.
The only issue with battery isolators is sometimes you'll see a voltage drop accross the isolator.
For battery switches there is allot of choices anywhere from $25 and up. I prefer the more expensive bigger Cole-Hersey switches compared to the $25 Chinese Blue Seas stuff. Although for $25 is looks decent and small in size for a small boat. But I think you get what you pay for too.
Good luck with the install, it is easy to do yourself.
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