The "crossover" relay on the Marinettes is not automatic: if you forget to switch it on, you only charge the starting battery, and if you forget to switch it off, the starting battery is pulled down with the house battery at anchor. That's why I bought the combiners: http://store.hamiltonmarine.com/browse.cfm/victron-combiner-isolator-cyrix-i-12-24v-100a-730942/4,39648.html
I didn't realize that you have a generator. That changes things. You only need for one of three engines to start to get going. If you keep a short set of jumper cables on board, you will be able to start anything from any battery. Wish I had one. I hope your batteries aren't in the engine compartment....
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida