Yes, do not wire them to your Nav lights. You need to be able to turn them off so you can run legal when navigating, then turn the fishing lights on when you stop to fish. If you have them on while running people cannot judge as accurately your speed and direction as they can when you just have your Nav lights on. Most people could care less it seems, but it's not legal to run with the LED's on.
But yes, point them down at the water if above the waterline. Most strips have something like a 120 degree projection, so they'll shine out a good ways as well as down.
If you're not living on the edge, you're taking up too much space!