Dave,
You need to have instruments on seperate battery from main engine, the voltage drop when turning starter is too much for the GPS etc to cope.
I have engine and associated instruments from panel (fuel gauge etc) on battery one and all GPS/sounder/CD etc on battery two.
I mean to get a more sophisticated diode controlled charging system sometime but for now I got the same as you describe so I usually cruise to wrecks etc on both, (or battery two to keep systems charged) then switch over to battery one for rest of the day. The hour or so at high charge getting to wreck in the morning is more than enough to keep the systems charged up, then the rest of the day starting and stopping engine whilst on battery one does not interfere with GPS.
Often forget and leave on battery one for weeks but you soon find out when finder turns itself off, simply turn to battery two or both for a short while and systems are back up in minutes.