I'm thinking of adding a sub and another set of speakers in the hatch area.

Current setup
Head unit - Sony CDX-GT700HD
Speakers -
Polk Audio DXi 6500 in the doors
Polk Audio DXi 650 behind the seats

The head unit has a Sub out, but I've been told I have to add an amp for a sub.

How would I wire up the 3rd set of speakers? Can I run them in series, or parallel on the rear channel of the head unit?

 

I would add the sub but not the extra rear speakers. The best sounding systems most of the time have just front speakers and rear "deck" speakers can detract from the overall sound. If you did put rear speakers in, the best thing to do would be to keep them as close to the same distance as the front door speakers. Hope this helps.