The first thing you need to do is charge the batteries and load test them. Plus you need to see what size you have, you may want to go up a size or 2 depending upon the size of your stereo and amps. The only problem with running the batteries on all is if they are EFI. Mercury tells you to run each engine with its own battery source for a few reasons, if the alternater takes a crap on one motor you dont want the other to have to carry it and try to supply both. That could leed to early failure of that one as well plus the performance may go down do to not enough voltage will be supplied to the ignition systems and computers.
I have a few customers that have installed a seperate battery for the amp and stereo so they can isolate it from the engines when sitting still. Run out with the engine and radio battery on all and switch over to the radio battery or batteries when you get out there. When coming in, switch back over the all position on that bank only. That way you charge the radio battery up on the way back in. If you are running a single engine it gets even easier. Run out or all over with the battery switch in the all position, when you get to the beach just switch one over to the biggest battery or one of them if there the same and use only that one. On the way in switch back over to the all position and run in.
If I am confusing you just give me a call at the shop or email me and I'll give you my cell.