(1) The factory amp is a POS. It's output is terrible along with high levels of distortion even at moderate volume levels. Bypassing it will improve sound quite a bit. You'll have much, much less distortion and more power for your speakers (better sound, bass response, and dynamic range). It's a great improvement for $20.
(2) Most aftermarket HU's have at least one set of pre-amp outputs. You can always "Y" them. I'd probably go with a deck with 2 sets of pre-outs. Many will offer sub controls for the rear set, which let you adjust the volume, phase, and x-over.
