Crossovers on HU can be useful if you have one of those "old" school type amps. They never came with anything. It is better to set the HU's crossover to flat or off and let the amps do it. That way, you will tailor the sound separately for mids/highs/bass or front/rear.
use the crossovers on the HU and turn off the ones on the amp if you can(unless the HU crossovers aren't very good) if not, set them the same. that way you are only sending the signals you need. having multipul crossovers processing the same signal can create distortion and other mess you don't want.
Would it be bad to use the rear speaker RCA outs to go to the subwoofer amp instead of the subwoofer RCA's since my HU lets me turn off the Front and Rear crossovers but not the Subwoofer crossover (only lets me select a low pass of 50, 63, 80, 100, or 125 Hz). I also have rear speakers so the rear speaker wire outs would also be used. Is this a good idea? Is there any problems with doing it this way?