Frequency equalizing -- Left and right channels separately or together

I have a Z-Systems RDP-1 parametric equalizer and enjoy the benefits quite a bit in terms of knocking down room modes a bit in the bass. One thing I have never been clear about is whether it is better to equalize each channel separately or to equalize with both channels operating together. I have always done them together and can't wrap my head around why doing them separately wouldn't entirely miss the issue of constructive and destructive wave interference the channels create with one another. In other words, the sum of the channel signals is different than adding the parts together because the signals from each channel affect one another when they play together, right?

I can also see the downside of equalizing channels together, because it assumes output from each channel is equal, which is certainly not true with many stereo recordings. So the "together" approach seems it has its flaws as well.

Also: I still use a Radio Shack SPL meter to manually measure test tones, which I know is not ideal at all. Would this whole issue be solved if I just borrowed a real time analyzer with pink noise and let it tell me how to set the RDP?

By the way, I have a rectangular room approx 16 x 29' and the subs are placed asymetrically. I biamp with two Vandersteen 2wq subs using first order passive crossovers (MP-5). Main speakers are Quad ESL-63s.

Thanks for any thoughts!