Good question. For years, I always measured at the listening area for each sub. It was a pain to match levels that way. Then it occurred to me when reading Dr. Floyd Toole's book that what matters is how the subs balance with respect to the room NOT the listening area. Remember in order to take full advantage of standing wave reduction, all subs must:
- be level matched with respect to each other
- be properly placed
- play exact same mono signal (LFE + all speakers set small)
The easiest way to measure each sub is to place the mic on the floor nearfield to the sub (within a few inches). If all your subs are single driver, then you can measure the SPL at the cone for each. You don't need to turn off the other subs if you do a nearfield measurement b/c the sound from that sub will dominate all others.
After you level match each sub, then go to the listening area and level match the main channels to the combined sub output. Once you flatten the bass of the subs, you can even boost their combined output a few dB over the main channels if you like.
Alternatively you can pick an equadistant point from all subs to measure their SPL individually but that can be difficult if they aren't all symmetrically placed in the room.