when you take your CD player out there will be a bunch of wires behind it.
Since yours is a 2000 I am not that familiar with By Passing the Factory amp on it.
But un hook all wires connected to your AFTERMARKET CD PLAYER.(Dont touch anything lese other than what is hooked up to your cd player now.) If there are more than one cables still hooked up let me know. ACT like your taking it out. Once you have all of the wires removed look in the back and there should be Two cables that are still connected. i am almost cetain that these are the Wires that connect the factory amp. Un hook these two cables.(Should just snap out) and hook the rest of your cd player back up and then everything should be fine.
trying to be as specif as possible