This did not even occur to me. Right now I have the gains set exactly the same on both. I have an android app spl meter too. I don't know about it's accuracy, but it should work for level matching. Great tip Shady.
If that is the only SPL meter you have, the way I would go about handling it is to connect the sub to a device that can playback tones, like a laptop or tablet. Use a tone generator, there are lots online like
this one. With both subs having the same gain knob setting, maybe at 9 o'clock or perhaps 12 o'clock, play back a series of tones to one sub at a time, and write down the results. I would try 25, Hz, 31 Hz, 40 Hz, 50 Hz, 63 Hz, and 80 Hz. When you have the SPL values written down for each sub, lower the gain on the sub that is getting more SPL until it is in the ballpark readings of the other sub. Remember the measurements have to be made in the same exact location, so don't move your android phone once you start taking the measurements.
Another way to do it is use a pink noise like
on this page. See what each sub is getting you individually with that noise, and then adjust the gain dial until they are giving you roughly the same SPL at your listening position. The pink noise is a more fluctuating sound, so you kind of have estimate the SPL it is hovering at.