I will be installing in a 350z and from what I understand is most guys with 350z's never run rear speakers. My question is...

Is there an internal x-over in the headunit itself? I would like to keep the rears connected and filter out the low...or is it even worth it?

Yes, the unit has a built-in high pass filter that will cut the bass out of the stereo speakers, be they connected via the unit's speaker outputs or an amplifier through the preouts.