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

JI use the DBX Driverack VENU360. It has 6 analog outs (xlr), four which can be used for subs. Each sub can be “tuned” to your liking with delay, polarity, dB gain, off/on all from your laptop, phone or iPad. You can also control your two mains with “Q” control, graphic and parametric eq’s as well as all of the above options. It also has a subharmonic control that can be very useful.
I’ve been very leased with the results.
Did I mention it also has a built-dac? I don’t use it, but it’s there if you need it.

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.