for your setup, i'd use either the xovers in the HU or on the amps, but not both. it can become messy if you use both and don't do it properly.
i'd suggest:
*HP the splits at 80Hz with 12~18dB/oct slope: what you have now sounds good; provides midbass through the front splits
*LP the sub at ~70Hz with 12~24dB/oct slope: a bit lower than the splits to avoid doubling up of frequencies being reproduced by sub/splits at the same time
time alignment is a great feature. read about it in the manual; no doubt it explains it there. because the front speakers are usually closer to your ears than the sub, i use TA to
delay the fronts, providing time for the subbass to 'catch up' and arrive at your ears at the same time. this provides much better 'upfront bass' (ie: subbass sounds like it comes from infront of your ears, not back in the boot) which is much more coherent. i delay my fronts around 5~6ms (milliseconds). you can also use it for L-R adjustment; cos the R speakers are closer to you, you can delay this a bit compared with the L, so they both arrive at the same time.; you usually need to delay the R (compared with L) by an extra 0.2ms or so, not much. but experiment. if you can't hear the difference, then your ears are not very experienced, in which case just leave it alone until you learn more.