You have to be careful with the head unit you pick out. I have listened to some "60 watt"
per channel radios that sound horrendous, and you replace it with a 15 watt per channel decent radio and it sounds much better.
The easiest way to put a sub and amp in would be to use a line level converter off the 6x9'* in the back, they are generally only getting bass anyways. Then you can keep your factory radio in as well.
The right way would be to scrap the entire stock audio system, but that is quite the financial burden, and takes a good amount of time.
COTY - 2012
Tom - 03' Bonneville SSEi', 00' Sierra SLE, 1980 Goldwing GL1100 Interstate