dont' leave it on both all the time, if you run down the batteries while on the hook you'll be dead in the water.
ideally, run on one battery one way, switch to the second one when you get there and run back on the same battery. this will insure both are charged and even if you run a battery down while anchored, you still have one fully charged.
if you switch while the engine is running, make sure you don't switch to off by mistake, that woudl damage the altgernator. many will tell you not to switch while the engine is runing, but that shudl be ok since battery switches always go to both between 1 and 2 so the batteries are always connected.
you could run on both to charge, but if one battery has a problem or is a little weaker, it's going to affect the other one. so unless you need to recharge both together, avoid runing on both