I currently have a pair of Martin Logan 212 subs which were middle of the road to set up. The software gets you in the ballpark but you really need to use your ears to adjust the phase and the output level. I am running speaker cables from my speakers to the subs and I noticed a big difference between the speaker cables I used.
Prior to the Logan’s I have used several different REL subs and I always found them the easiest to integrate. I wanted to go with another pair of them instead of the Logan’s but the retailer I buy some of my gear from doesn’t carry REL. The Logan’s sound really good but they take a little more work to dial in than the REL’s.