stlhead,
I run two seperate batteries, but really for no particular reason. I think it is just personnal preference. I put a seperate battery in that only runs my downriggers but I don't have it connected through a switch to my other battery so I can charge it with the motor. I just didn't want to take a chance of having a downrigger problem screw up my electrical system on my motor. I just charge the downrigger battery in the garage when it needs it, and I can get three day trips and sometimes four on every charge. Of course that all depends on the battery you use, the downriggers you have (I use Big Jon downriggers) and how heavy your rigger balls are.