2000 mustang?

if it's just the "premium" sound system and not the "mach" sound system, then there is a single factory amplifier.  It is located underneath the cd player underneath the dash.

Please whatever you do, if you're keeping the factory cd player and deck, use the right amp integration harness.   I made the big mistake a while ago of NOT doing it this way and have had nothing but trouble with it ever since.  Customer has been back many times and the system still sounds like poo.

I'm pretty sure the one you'd need would be the FDK3.  The FD04 part of the kit would be what you'd hook the aftermarket amp's signal inputs up to.  The FD05 part is how you'd send the amplified outputs of the aftermarket amplifier to the factory speakers using the existing factory speaker wiring.

If it DOES have the mach system, I hope you can return your amplifier.  lol no it really will be more hassle than you could imagine.  There are three separate amplifiers in the mach system--one under the dash for the higher frequencies, and two on the rear wheel hump or under the rear deck, for the low frequencies.  Also the turn on for the aftermarket amp would have to come from some other location as the remote turn on for the factory amps is not the 12 volts that most aftermarket amps require.  There are ways to use relays and such but that's a lot more work.