I have an amp added to my Stock HU and it sounds just as good as an aftermarket. I should know I had three different setups in my car in just the past month.
1. Stock HU with an amp that has high level inputs. Sounded ok, didn't have quite the punch I thought it could have but it was enough to satasfy my crave. Had this setup for about three years.
2. Aftermarket Pioneer Premier DEH-P750MP HU with RCA connection into amp. Deffinetly a better sound than the previous setup, A lot more bass and sound control due to the options on the HU. Was quite satasfied, until some jackass was also admiring my HU and stole it.
3. Back to Stock HU with RCA connection. Decided to install it like this because I had the RCA's ran. To do this I installed one of these
N-85V from David Navone. It brought the stock HU setup up to aftermarket quality. Plus I have the ability to adjust on the fly with this item. Was definitly worth the payout. Plus I have a good sounding system with out the worry of it being stolen. I've got more thump than I ever need.
If you are looking to keep the stock HU this is the best option for an amp install. Just ask me anything about the wires and i can tell you exactly what to do. I can even tell you how to install a 2001 and newer RDS radio in your 99 and 2000 cars, that is was I have done. I like the look of these radios better.