Wayne,
You should connect the battery switches so that either battery can connect to either engine, or both. The way I did it is shown at
www.geocities.com/dougmrose under 32 Marinette Wiring.
If you can't start an engine, swap batteries to the opposite engine and try again. Check the alternator and the battery. If this doesn't work, parallel the batteries to get start current and then fix!
Otherwise, you should only use "Both" when engines are running, if then. I would not use an isolator, I would use a combiner like
http://store.hamiltonmar.../browse.cfm/4,6007.html . it is expensive, and when I have time I will make my own.
The only problem with combiners or isolators is that you can lose an alternator and never know it. If the systems are separate, it is pretty obvious pretty soon.
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida