Pop the negative battery cable off, hook the meter inline with the battery and the negative lead. Hook the black lead to the battery cable and the red to the negative battery terminal (If I have that reversed you'll just see negative values). Make sure you have everything off, doors shut, etc. or you will blow the fuse in the meter.

Set the meter to mA and read how much is being passed through the system.

 

It's not going to be fun without a schematic, but you'll need to measure power on *each* lead to see which get's constant power (tag them). Then turn on the ignition and check which wires get switched power (tag them). Then turn on the radio and see which lead (should only be one) gets power to turn on the amp. My guess is that last lead is switched with another wire of the same color.