Mike,
My battery started draning too after I hooked up the big power lead to my 1000 watt amp in the trunk. If you don't like disconnecting your battery all of the time and losing your saved stations, go to an electronics junk store and look for one of those 12v relays used in some of the smaller cars as starter or load carrying relays. You can also order one from an electronics store like Digikey. These are not the small ones like the ones used for headlights.
Then hook the trigger to your switched amp wire from the head unit. It will turn on the big red wire to the amp.
If you can't find one of the big ones cheap, you cam probably use 3 of the 30 or 40 amp (small ones from auto parts), wired in parallel to carry the load.
If you want to "see" the current draw without an amp meter, use a small light bulb between the + battery post and the + car clamp. The brighter it glows, the higher the draw. This would also help find shorts. You start unplugging parts of the harness till the light goes out.
