a few comments here... 1st, measurements *are* crucial to get a good starting point, imo... it will save lotsa time in fine-tuning. i like to use an equalizer/spectrum analyzer w/pink noise generator & mic to dial in the initial sub-to-monitor relationship. then, tune to ear. also, you will get far better results, imo, w/a hi-quality outboard x-over, than what's included in the sub amp.
re: not getting as good results w/one amp vs another, this is also not that unusual. some speakers will react differently w/different electronics, in different set-ups. again, using measurement dewices will get you much closer to flat, from the start. also, perhaps, in your case, the amps have different phase?
i know, that when experimenting w/different speakers in my system, in one case, (swan m1.2), i actually got better results w/my diminutive modded asl wave-8 8wpc amps, crossed over at 125hz, than w/my mesa baron, my normal amp. and, normal x-over range w/other speakers is 50-70hz... the swans had a mid-bass bump that was ameliorated by the leaner bass of the li'l waves, & the vmps larger subs are actually more lean & tight between 50hz-125hz than were the swans... this was actually wisible on the spectrum analyzer... the waves are down in output in the low end, & the swans midbass was a bit elevated... and, of course, the wave's, at only 8wpc were happy to not have to deal w/any frequencies <125hz.
doug s.