Stereo & Electronics - Do I keep the factory Monsson amp or not?

I am installing an aftermarket deck in my TA that will have atleast 50 watts along with an Alpine 10in in a stealth/subthump box. I was also going to remove the factory sail panel subs and pull the wires from the trunk speakers forward and installing some nice 6.5 coaxials where the factory subs were. Should I run the system without the factory amp or should I keep it? I'm not sure if the quality of the amp will hurt the performance of my new setup.

Given a choice between running directly from the head unit (just about any head unit) or retaining the factory amp, I would stick with the amp. It won't hurt your sound quality (the factory HU does most of that) and it will give you some additional power.

Now, if you had the choice of replacing the factory amp with a better aftermarket one then that would be the way to go.