Help Frequency Hole - Processor? Diva?

You can hire a professional (cannot help with that) or you can undertake the project, if you have the inclination and time. There is a very useful tool called RoomEQ Wizard which is freeware and you would only have to buy a mic and preamp or, at least, a Radio Shack SLM. There's lots of help and discussion about this and its applications at:
http://www.hometheatershack.com/roomeq/
http://www.hometheatershack.com/forums/rew-forum/

Kal

Thanks Flmlamb. It sounds like I need a pro. Do you have any recommendations on who could help solve my problem?

Another problem here (sorry, didn't read you whold post) is that you likely have your two subs out of phase, in relation to where you sit, and were the main speakers are located. I've seen this on occasions, actually. Infact, I fixed a trained lisenced installer's system, that had the very problem (among others), where his two several thousand dollar subwoofers weren't producing hardly any bass in the system. Also, his mains were in a place where they weren't coupling well at the critical crossover frequency, between speakers and subs.
All this compounds things. You should get the main speakers balanced from the listening position first, then the subwoofer, then tie them all together, and let the processor handle phase, and level matching - in your case.
Try this: Until you get a sound meter and test disc, you can simply try placing one of your speakers (woofers) where your head will be in a chair (listening possition). Then, listen to some mono-summed (or stereo, if must)music with a steady bass beat, that you KNOW sounds like there's a "hole" when you play it. Then, go listen from where the speaker originally was, placing your ears near where the woofer on the speaker used to be placed. Then, move around the space a bit, until you hear a place where the bass is more solid and there's no hole!
This step should be done first with the main speakers, playing full range. This way you can identify wether the problem is in the main speaker locations (also, the listening position, as they're directly correlated). Do this also with the center, and rears.
Then, do this with the subwoofer, place where your chair is, ear height. Listen for solid bass. Then, I'd suggest placing the two subs either on top of each other, or right next to each other, for best phase cohesion with mains, no matter where you sit in the room!
If you place the subs in half spots around the room, it's going to be hard for you to get phase right, and you'll running into phase cancelation problems, unless you know what you're doing.
Setting up a properly balanced and coherent home theater is not an easy task for the inexperienced. As you can see, there's lot's to know.
Hope that helps, good luck

I agree with Flrnlamp - the golden rule with EQ is "Do not boost for nulls"...so alternatively try different placements and EQ to tame the peaks - also room acoustic treatments can do a little to help to get a smoother response....but room modes are likely the source of your issues.

No processor or EQ in the world can fix a "hole" in the sound!" (I take it back - readjusting phase between speakers and sub, or two subs, can put back the frequency that might have been cancelled out, in a poorly arranged setup).
For the most part, a "hole in the sound" is usually always a frequency response problem, due to a "null" from bass modes in the room. And either/both you and the speaker(or sub) possitioning in the room is the culprit!
What you need to do is place a speaker in the corner(whichever speaker or sub is handling that/those frequencies, or both), get a sound level meter, play some testones (or at least some program bass material that covers the frequencies in question well), and move around the room till you find where your nulls and peaks are at that/those frequency(ies). You can then better identify where your nulls are, and then DON'T SIT OR PLACE YOUR SPEAKERS IN THEM!!!
If your room is indeed perfectly square, you have major reinforcement of the bass modes, and peaks and dips (holes) will be magnified, yes.
You can go on to www.ultimateav.com and use the bass mode calculator for your room dimmensions, and that will tell you what modes you're predominently dealing with.
Good luck