Charge, keep charged, discharge
It is best to completely charge a deep cycle battery before installing it in your boat. If you have a good automatic charger you can rely on that after installation. As Steve said, a deep cycle battery should be kept charged when possible. Of course, you will have some discharge when using your 12v system when not charging with either the shore power charger or alternator. At that time, if possible, it is best to keep from discharging the batteries below 80% and/or keeping them discharged at lower levels for extended periods of time. Throw into this mix that it IS good to discharge the battery occasionally to 80% if you are constantly charging them and keeping them peaked. This has something to do with the health of the battery and it's "memory". There is tons of info (and conflicting opinions) on the net, but this summarizes it.Chris