I wasn't refering to lack of horsepower of the room correction but rather its lack of ability to EQ the subs individually (which most not-super-expensive systems can't do).
What i usually do first is I align the phase of the subwoofers by aligning the phase at the frequencies below the first room mode. phase should be fairly clean there.
Once the phase is aligned and the subwoofers are gain or SPL matched it should be more or less fine with just a singular global EQ.