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

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.
 

These are  great suggestions and I really appreciate them. 
For the moment one thing is absolutely certain : with 6 1/2 foot ceilings there is no way that I am going to get a great result even with the technology you are mentioning. At this point my best option is to try to learn how to optimize my room with what I have. Because even if I have a more sophisticated tool it is only going to drive me toward recognizing a foregone conclusion, namely that I have the limitations that I’m already close to confirming, I believe. When I am able to move rooms, hopefully in a year or so, these tools may be much more appropriate.

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!!

Low ceiling is a challenge the first consideration would be get a speaker with a very narrow vertical dispersion and have the listening position nearfield. 

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