Headunit crossovers usually filter the cut frequencies to a sub/rear output. So, if you crossover at 100hz, everything over will go to your doors/deck. Everything under 100hz will be sent to the sub or rear output, depending on the head unit. If you aren't using the sub or rear output correctly (sounds like you aren't), you'll hear the lower frequencies drop off.
I usually let the headunit do the crossover work and set the amp's hi pass as high as it will go (usually 200hz) so it is completely allowing the HU to cross over the frequencies. They build them into amps for when your headunit doesn't support it, or you are feeding line level inputs (from an amp) to the sub without being filtered first.
