AutoEQ only works for daisy-chained subs. However, for the purposes of set-up you can daisy-chain them, run AutoEQ, and then connect them in stereo if you desire.
I should mention that I'm very unimpressed with AutoEQ. It does not produce anything like a flat in-room response. I recommend buying something like the Parts Express OmniMic system and measuring for yourself, using 1/12th octave smoothing. You'll have to tune things manually, but the best tuning is done by placement and some judicious equalization anyway.
I highly recommend reading the excellent review of your sub on the audioholics.com web site.
I should mention that I'm very unimpressed with AutoEQ. It does not produce anything like a flat in-room response. I recommend buying something like the Parts Express OmniMic system and measuring for yourself, using 1/12th octave smoothing. You'll have to tune things manually, but the best tuning is done by placement and some judicious equalization anyway.
I highly recommend reading the excellent review of your sub on the audioholics.com web site.