I don’t see why it should be a problem. The BFD has two channels. Just dedicate one channel to each sub. Or, if they’re both fed by the same sub out from the receiver, just insert the BFD in front of them, just like you would do with a single sub.
If the delay becomes an issue, you could switch to another equalizer. My Yamaha YDP2006 has independent delay for both channels; I believe some of the Behringer processors do, too.