Many of the phone mics don't measure sub bass output very well, if it all. So it could easily be throwing off your setup efforts.
Most room correction software does more than simply measure output and set channel levels. It also adjust time delays and EQs the speakers--something you can't do at all with an SPL meter with the timing, and it would be a pain to set the EQ unless you like running frequency tones and trying to measure.
And you can level match your subs with YPAO. If both your subs were turned on and level matched such that YPAO determined a subwoofer channel level of 0 db, then if you turn one off, you ideally should end up roughly at -3db. That's what you get from having the extra sub.
So measure one sub turned on with YPAO and adjust the gain until it's at -3db. Turn it off, then measure the other sub with YPAO until it's at -3db. Then turn them both on and measure again. Now there might be some variation, but that should get you pretty close, much close than a phone SPL meter