What process did you use to integrate multiple subwoofers for 2 channel listening?

MiniDSP 2 x 4 HD, a calibrated mic ( Umik-1 or Dayton ), a db measurement tool of your choice ( decibel: db sound level app on iPhone is great ), REW app on your laptop, YouTube tutorial Episode 7 from "Hometheatergurus" channel ( along with the gain matching episode )  and you will get absolutely amazing results if your willing to go through the headaches of a learning curve. 
I have a Focal 1000F, Def Tech SC4000 and an old Def Tech SC-1
 ( how's that for a crazy ridiculous mix?!! ) and it literally sounds like I have a single subwoofer from the main listening position. The SC4000 is only about 5-6 feet behind the listening position so occasionally ( but rarely ) I have to adjust the volume but it has remote control and through my Harmony hub it's easy as pie to do.
  MiniDSP allows for 4 configurations ( again controlled through the Harmony hub ) that I have set from flat response to a couple of different mid bump options to play with depending on the movie or music track and my listening whim at the moment. 
  A long time issue I've dealt with from just one to two to three sub configuration is now a mute point. Although nothing is perfect, the technology available is a wonderful tool if your willing to give it a try. I guarantee it's better than any " by ear " method, I don't care how good your ear is or how long you crawl around your room. Your just finding bumps in frequency at different areas of your room and not flat response anyway . There are too many factors so let technology be your friend. You ( and your ears ) will be glad you did.

P.S. - room treatments would be a great addition to the equation. That will
         be my next step hopefully.

REW can do so much more when implementing the MiniDSP along with it, it's not just a sweeping tool, it's an all in one turn key solution. The Driverack is a great piece of equipment, I used the original 360 model back in the day in a professional environment,  but you can do all the things ( and more ) the DBX Driverack can for 20% of the price with REW ( free ) and the MiniDSP ( $205 ) for up to 4 subs.
You measure each sub separately then measure them all together ( gain matching should be done before you start ) and you can see the difference after all have been measured together. Then you start delay comparisons ( with sweeps ) and after you find the best combination of delays you go to the EQ section of REW and that's where the magic begins. You create a room curve of your liking ( you don't want total flat response ) and after going through the settings then hit the "Match the Target" and REW equalizes your original measurement ( of YOUR room with all it's acoustic anomalies )  to the "room curve" you've determined. It has used a 10 point parametric EQ to do it ( including Q control ) and you can continue to manipulate it ( and if it didn't use all 10 points you can add to it ) to make it better.
I'm sure you have had successful  improvement from just using the sweeps and adjustments you made but REW / MiniDSP will take it to the point your attempting to get to. You will be absolutely amazed and will enjoy your 2 channel system in a way you hadn't even imagined.
 

Excellent point about your ceiling height, I should have thought about that and asked ( or maybe you mentioned it in an earlier post and I missed it ) because I do benefit from having 12 foot ceilings and though obviously  being a completely different animal when I went to Atmos surround I knew immediately the ceiling speakers integrated well for that very reason. I can just imagine the challenge of dealing with just 6 1/2 feet overhead!!

djones51,
He is dealing with subwoofer issues , not mains.

Yeah, Sliders , one of those inventions that are so simple but so ingenious.