If I had the room I'd probably run a second starting battery with the off, 1, 2 and 1&2 switch and leave the set up as is. If not I'd look to utilise my deep cycle battery more. There are others on here far more knowledgable about this stuff than me. Going by your description it's a first line safety system that must work so I would err on the side of caution.
I was out from 4pm to 2 am the other arvo night with live bait tank, sounder and Nav lights running with no dramas on my first battery, no signs of going flat. ( boat is Stacer 5.7 with 150 etec). We did do a few short moves whilst drifting and a run in from the heads to Yowie bay to change spot. It's good piece of mind having another fully charged battery ready to switch over.
However the first thing I would do is have it on trickle charge and make sure I'm leaving home with a fully charged battery.