If you are going to operate the switch manually then the best thing to do is to start off of one battery, then once the engine is running switch to ALL. I prefer starting off just one battery (verses starting on ALL) just so that you know that the battery you started off of is OK.
Once you shut the engine off you must turn the switch to 1 or 2. If you have a battery dedicated for "deep cycle" switch to that one.
Caution: NEVER move the switch to "OFF" while the enigne is running. Doing so can destroy your alternator and/or any electronics you have operating.
Note that if you forget and leave the battery on ALL once you shut the engine off then the benefit of having dual batteries is mostly lost.
The best thing to do is to get a "battery combiner" that takes care of the switching automatically. Here is a good one (but perhaps is a bit of overkill):
http://www.westmarine.com/webapp/wcs/stores/servlet/ProductDisplay?storeId=10001&langId=-1&catalogId=10001&classNum=12106&subdeptNum=544&st oreNum=9&productId=144540