Just connect it up to the negative on the battery. Bruce, you can do this as a 3 minute test just to see if it helps next time you go boating. Just get a piece of wire, maybe 14 ga. or heavier. Could be speaker wire if you have some. Just twist the end around the clamp down screw on the battery terminal and then while you're running the engine and hearing the whine, touch the other end of the wire to the back of the radio chassis. If it doesn't go away, might not be the problem but it's a really simple check.
I guess the other thing is to make sure that you have the volume of the iPod turned up pretty high. I don't go quite all the way up on mine but about 7/8 or so. If the iPod output is too low, then you'll really have to crank up the radio amp to hear it and that might not be the cleanest sound.
I'm betting the ground will help. If it does, then just get a nice piece of black ground wire, maybe 12 ga. and put a ring terminal on the battery end and connect there. Then, run along the gunwale to the helm. Find the black ground wire coming off the radio harness. Cut that and use a butt connector there to make that connection. Should be golden.
O'
"Little Mascara 3"
2003 266BR,496 MAG w/Bravo III