I don't see a problem putting a battery in the bottom of a boat like the C D 22 (the battery goes into a box. If you have 11 inches of water in the boat, you are going to have a lot of problems, and placement of the batteries may not be the most important. Batteries down low, keep the weight low. However, in the 22, I did have one battery in a lazarette and the second, was under the sink.
If the battery switch is make before break or has a field disconnect, you can safely switch the battery from #1 to both. You have to have the ouput of the alternator going to a load/resistance, or cut alternator output (field disconnect). Double check the switch--most of the combine switches are make before break, so they are safe.
There is a potential problem with the battery switch on "both" when you have unequal batteries. The assumption is that one battery will have a lower capacity than the other. The lower capacity battery can be overcharged and thus boil off water. It would be better to have a dual output battery charger, which isolates the two batteries with diodes.
If the battery switch is make before break or has a field disconnect, you can safely switch the battery from #1 to both. You have to have the ouput of the alternator going to a load/resistance, or cut alternator output (field disconnect). Double check the switch--most of the combine switches are make before break, so they are safe.
There is a potential problem with the battery switch on "both" when you have unequal batteries. The assumption is that one battery will have a lower capacity than the other. The lower capacity battery can be overcharged and thus boil off water. It would be better to have a dual output battery charger, which isolates the two batteries with diodes.