All depends on your unit. Some will let you set up crossover for front and rear channels independently, others won't. (My alpine did not) To be safe I would just use the sub outs as they should always have their own crossover settings. Also the stock amp has its own built in crossover for the subs so even if you hook the rears to the rear outs you will not hear anything higher frequency than the built in crossover. (Not sure what the cut off is)

My setup with an alpine
Front pre-outs directly to amp front input
Sub pre-outs directly to amp sub inputs

I can't remember the exact settings but I think I had the front crossover set to >120 and bumped treble up a couple tics too which gets rid of a lot of the door bass (and rattle) and cleans up the highs. I just left the sub crossover as is because the amp is doing it anyway but I increased the sub volume to almost max (note my head unit was only 2V output) which supplied the bump and lows. Sound is much better than stock but max volume is lower because of the 2V (at max volume sound levels were right before it starts to get distorted or rattle so it worked out) but I do wish it could go a liiiitle higher as my source is majority iPod and levels on some recordings are a little lower than others.