You have to wire the amps so that you can disconnect them when not using the boat (or the amps will drain the batteries), and decide if you want your alternator to be able to charge them.
You could use an isolator to isolate the two stereo batteries, and run them on a separate Perko switch, or you could just wire the amps to a single Perko switch, and wire the starting battery to #1 and the other two in parallel to #2.
Then, if you run the tunes without the engine running, just switch to #2, so you have the starting battery fully charged when it comes time to leave.
Those are two ways, but I'm no expert (just an internet journeyman wire jockey).