u should be ok as far as signal going into the amp, but like in the other reply alligator clips aren't a great permanent connection. i used wiretap clips in my installation.
yea it will work. What he is wanting to do, as i take it anyway, is hook up a LOC. Why would it make a different if he tapped into the wires right behind the headunit or right before the speakers. Ive actually done it this way before. The only con to doing this is that if you ever adjust your balance, it will effect you sub. But if you dont ever mess with that you are fine.