I do not run near as much with my cranking battery as Hooks. I have not yet removed my 350a from the battery and have never had any problems draining the battery. I just run the Areators on auto, 350a and GPS, and a Flasher up front. I will often run for 8 hours and no trouble except when I turn the key to start and it does not matter where the battery charge is then, the GPS will kick out.

What does the screen show if anything? I have a 350A and my GPS seems to work very well. I have noticed that if you have it wired to your dash power switch, every time you start the boat with the 350 already turned on, you will loose GPS signal and it will take a long time to get it back. Two solutions: First, if this happens, shut off the 350A and turn back on, the GPS will lock faster that way. Or wire it right to the battery so you do not get a voltage drop at the 350 upon start-up.
Just a couple thoughts.