1) if your room is an enclosed rectangle, put the subs directly across the room from one another. Mid-points of opposing walls is best. Diagonally opposite corners is 2nd best.
2) Feed them both the same signal (mono).
3) Level match them by using your Receiver’s built-in test tone. Set the Receiver’s master volume to 0dB (very loud), set the subwoofer trim level in the Receiver to 0dB. Temporarily connect only one sub and adjust its volume dial until your SPL meter (C-weighted) reads 72 dB at your primary seat. Then disconnect Sub1, temporarily connect only Sub2, and repeat – adjust Sub2’s volume dial until SPL meter reads 72dB at your seat. Then connect both subs. Playing in mono together, they should read ~75dB at your seat now.
4) Run your auto-setup as usual. Since the mono subwoofer signal is being played by two subs that are across the room from each other, you might get an odd looking setting for the distance. Leave that alone.
5) If your room is not an enclosed rectangle, or you simply cannot position the two subs directly across the room from each other, then still try to position them roughly across your space. Try not to have them both on the same side. Spread them apart as much as possible.
6) Level match them – same procedure as above
7) Now, figure out which sub is physically farthest away from your main seat. Set that sub’s phase knob to 0°. We’ll call this Sub1.
8) Start with the Sub2’s (physically closer to your main seat) phase knob at 0°.
9) Play a bass sweep on repeat (you can download a bass sweep from audiocheck.net , or just play one off of YouTube on repeat)
10) With the bass sweep repeating, move from seat to seat (every seat you care about, but nothing way off to the sides. Think 3-seater couch). Listen to the sweep. What you want to hear is uniformity. Not necessarily linearity at this point. Some humps & dips in the sweep are ok. But you want the same humps & dips in every seat. Uniformity is the goal.
11) Adjust the phase knob of Sub2 only. Ideally, do so 3° at a time, although that can be very tedious, so you can start with 6° at a time and possibly fine tune after.
It’s just trial & error. Adjust Sub2 phase knob, listen to sweep in all seats, try to find uniformity (although no total nulls. If it’s uniform, but you have a full on null (silence) at some point in the sweep, then you need to keep searching). Repeat until uniformity is achieved!
12) Once you have uniformity, run auto setup. Again, two subs are playing the single subwoofer output in mono, so expect a strange distance setting in the Receiver.
Lastly, manually set all speakers to “small” if any were set to large by the auto setup. If auto setup set the crossover frequency of any of your speakers higher than 80Hz, leave those alone. If it set any crossovers lower than 80Hz, manually raise those to 80Hz.
That should do it!
As a final note, if you want to set up three or four subwoofers, check out the Multi-Sub Optimizer Software.