The head unit should be left flat for the low frequencies and all adjustments done on the Amp. The Hi-Low converter just changes the speaker output to low voltage for the RCA input to the amp, not the audio frequencies.
The Amp does a lot of the heavy lifting with the audio filtering so adjusting the settings on the head unit creates unexpected and unaccounted changes to the audio profile which can be incorrectly amplified by the Amps design and can cause unexpected defects in audio quality and poor performance. Plus, it can shorten the life of the speakers.
Some amps actually have built-in Hi-level input, which usually create less "noise" than using a Hi-Low converters giving an overall better output quality.
Either way, your adjustments to change the Sub behaviour should be done at the Amp using the LPF and other adjustment features it has. You haven't told us which make and model the Amp and Sub are so can't
help further.