I run 3 batteries. I've got 1 starting battery that is only responsible for starting and running the stuff wired through the dashboard. The other 2 are large, deep-cycle batteries that run everything else (stereo, pumps, etc.)
I recommend the blue-sea add a battery system (
http://www.bluesea.com/products/7650) because it keeps it WAY simpler as far as automating your battery switching. When the boat is running, it combines the battery banks so that both of them charge. Without this, you have to manually switch from 1 to 2 to make sure your batteries stay charged. It's a PITA. It also comes with a nice PERKO style switch (although I think it's nicer) that allows you to turn both banks completely off, or combine them (when your starting battery goes dead, you want to combine both banks to start the boat.)
I fiddled around with all kinds of electrical problems before I sort of started over and spent the money to do it right. My batteries are probably overkill for most systems but I am running a lot of power. All of my wiring is 0 or 00 gauge. I also installed this on-board charger (
http://www.amazon.com/NOCO-GEN2-On-B.../dp/B003JSJS5I) and it makes sure all of my batteries are always charged/maintained properly. I just leave it plugged in whenever I'm not on the water. I had the ProSport version of that before and it burned up -- I've been pretty happy with this NOCO model.
I also installed a 160 amp alternator to make sure I was charging batteries as much as possible while running.
I haven't been stranded with a dead/dying battery since upgrading all of this. I use cheap Wal-Mart batteries and they have all lasted me 3-4 years on average.