Turn your HU's LPF to its highest setting... then adjust with the amps LPF. This will give you the most flexability with cutting frequencys out of the subs. The
18db/octave filter wil be better than the HU's anyways.
-However if you like driver seat tuning, completely reverse what I said. The amp at highest point, and use the HU's. It might just not integrate very well with the rest of your system given the default freqs.