L33.H

It does have an amp in the left hand corner behind the glove box, iv found out now that i take one or maybe two of the plugs out of the back of the amp and plug the bypass wire in to the plug I have taken out of the amp, the other side of the bypass wire plugs in the the stereo, does this sound right? 

I need someone to help me, I would appreciate it so much, I have a lexus IS200 se year 2000, I have bought a jvc stereo which came with a wiring harnes, I then ordered a fascia that comes with a harness that would go into the harness that came with the stereo, but it doesn't fit it the the plug that was in the standard radio, i don't really want to bypass the amp either, is there anything I can do here ?