I bought an aftermarket HU (Sony X-Plode), did the install, and I like the sound and everything but, I want to know if the 200Watts from the HU is more than what the factory amp is pushing (HU has a built-in pre-amp).

I guess this leads to a more specific question: What is the watt rating on the factory amp in a '99 Bone?

I also want to know if anyone knows how to bypass the factory amp. Do I have to buy an adapter or can I just disconnect the amp and hardwire the speakers?

check out impalahq.com http://impalahq.com/HowTo/Amp_bypass.html
should give you some ideas i am however unsure if it is the same amp

you HU is NOT putting out 200W....its lucky to be putting out 15 per channel to the speakers....the Bose amp is NOT holding you back its prolly putting out more than your Sony HU.....i recommend using the factroy amp with the HU...as the Bose only amps up the base in the rear speakers....

C'mon now, it'll probably do 50w peak x 4 channels, but no, it'* not 200w RMS. Unless I see some bench testing, If it'* anything like the Bose in the home audio world, it'* junk, doesn't work well with conventional equipment, etc...

With respect to your setup, I would bypass the amp once you have aftermarket speakers to put in. In that case the optimal solution would be to run completely new speaker wire from your Head unit harness to the speaker leads.

i have some input on this.... i have a pioneer 7800 50wx4 peak.. blah blah blah and i had the same problem with factory amp, it would cut out on me all the time... so i just sent hardwires from my deck str8 to the speakers. couldnt be happier...