Also consider twisting the pairs of speaker wires. Telephone and network cables are done like this to minimize or even fully protect against stray noise. You can also use a "ground loop isolator" which plugs into the rca inputs of your amp in case you are picking up noise that way too.
If you have time for some troubleshooting, do this:
Unplug your RCAs to the amp, then turn on the car. If you still have an alternator whine, then your internal noise filter in the amp is probably shot OR your wires to the 6x9s is picking it up from the power cable. If it goes away, then your RCA cables are picking up the noise...upgrade to RCAs that are shielded or get that ground loop isolator I talked about, or try running the RCAs and the power cable on opposite sides of the car.
Hope this helps ya.
Welcome, downwardly mobile yuppies, to the dawn of the Age of Nefarious.
1993 SSEi - FrankenJinx - dead and gone.
1994 SSE (136K strong) - 180* t-stat,HD alternator, most unequipped SSE on the club, XM radio, Kenwood CD/MP3.
2006 Chevy Malibu Maxx LTZ - Custom 2.25" manifold-back exhaust w/FM-80. Probably the only Maxx with this system.