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What I have described is the standard for wiring dual batteries in small craft (23ft or less) with a single outboard. Typically what most people do is switch batteries durring the day. Some will run out on one, fish, then at some point, switch to two and use two for the run back. I usually alternate between main batteries each trip.
YOU DO NOT WANT TO RUN ON BOTH. If you have a problem battery that is not holding a chage, and you run on both, it will drain the good battery down to the charge of the bad battery. This is a fact. you will then be screwed with two bad bateries. Charge one, and then charge the other. If you are not able to start on one, then try the other. If you can't start on that one, then use both. That is the only time to use both.
You can wire like mike said with an isolator, but that is typically only used on large boats where there is a major drain on the house battery. For small craft it is not necessary.
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