Here is how I use my "old school" setup. The comments about more modern setups are well taken but assuming you'll be using the old 1,2,both switch for a little longer :
If the batteries have been sitting under an A/C charger so you are starting with them fully charged : When starting and under way, set the switch to 1 or 2, depending on the date. Odd dates, set to 1, even dates set to 2. That way your batteries get even usage, averaged out over the year.
The only circumstance when "both" should be used is an emergency when one battery will not start the engine. It should not be used under any other circumstances. "Both" should really be labelled "Emergency"
Obviously when overnighting, you'll want to drain the deep cycle battery (2?), keeping the starting battery (1) for reserve. In that case the next morning select 1, start the engine, run for 10 mins, then switch to 2.