1) In some (maybe even most) cases, the phase control is
enough, especially for low frequencies.
2) You can equalize the sub either in the sub itself (some subs have this feature), or you can equalize it in your computer digitally even before the signal goes out to the DAC.
3) You can also adjust delay / phase / eq fully in the computer before the DAC.
I used the REW software and RePhase software to create a single correction impulse for my 2.1 audio setup to do digital room correction and to correct both the phase and frequency anomalies. For each channel separately.