Can I replace the Bose 6x9's in a 99 SE with aftermarket speakers without messing with the head unit? If anyone knows a good brand please let me know. Thanks.

Two off the top of my head are the JL Audio Evolution TR690 and the Eclipse 3 Way 6x9.

If it is a BOSE system, you cannot. The ohm rating for the BOSE is WAY under what normal speakers run at. YOu can upgrade the Headunit with the aid of adapters, but not speakers. Ther is an online company that I cannot remember the name of ( maybe someone else remembers) that sells replacement BOSE amps and speakers....