You should have bypassed your factory amp when installing the new aftermarket headunit. If you hooked up the factory amp inline with the new HU and speakers then your system is not installed correctly.

The factory amp utilizes the same logic as aftermarket amps when installing. There are a set of inputs and a set of outputs on it. The RF HU is connected to the inputs on the amp and the speakers are connected to the outputs of the amp. Essentially, you should tap into the speaker wires that are connected to the factory amp's outputs. Your factory amp should not even be hooked up to anything, it should just be taking up space.

To locate the factory amp remove the plastic molding that surrounds the stereo. Down on the floor is a plain, silver box about the size of the original RF HU. That is the factory amp. If there are any wire harnesses connected to it then disconnect them, locate the speaker wires and tap into those directly from the new HU.

If the distortion problem is happening only at loud volumes you may be hearing a clipped signal. If this is the case then playing music at those volumes will damage the speakers and eventually blow them.