I would use a single channel eq.
Explanation as follows...
Bass modes and standing waves will be location dependant....what I mean is this:
Standard one sub: start by finding the sub placement that gives the flattest respose in your listening position. (usually a corner and a couple inches can make a large difference). It is important to remember than small changes in seating position also have a profound effect on the bass. A foot to the side and whole other frequencies will be affected.
With two subs: try to have two that are the same, having two different types of subs not collocated will make eq'ing very difficult. The placement can get even trickier with two because now you have another variable. However, it will allow you to use placement to get rid of your worst nulls. After you have the placement down and the best freq response you can get...then use the eq on the pair. Always try to get rid of peaks by eq, nulls by sub position, if you eq out a null (where you have a standing wave) you will drain you sub of tons of performance.
I am assuming you are using the subs in mono? When you get into a larger room and trying for stereo bass it is more difficult and you will have to get someone else to fill in.
Also a quick plug, the Behringer (sp?) DSP 1124 is a great piece of equipment to eq a sub, highly recommended. Has 12 bands X 2 channels of parametric eq (pick band width, freq and boost/cut) for about $100. I am at +/- 1.5 dB from 25 to 80Hz using only 3 bands (the magic of parametric). I had a 18+ dB swing before from 45 to 55 Hz. You can really tighten up bass transients by fixing these problems.