Speaker level EQ

There are great sub dsp solutions, but they won’t work for you. With two subs, you should be able to address virtually all room modes at your listening position by placement. I would get room eq and purchase the needed microphone ($60) as it makes it much faster to measure and test the effects of moving your subs, as well as changing their polarity. If you are still having issues, adding a third well placed sub is probably the most cost effective way to lessen the modes.  

Also, room eq will allow you to view your decay time at various frequencies and use targeted frequency bass traps for modes and slow decay.  

Alternatively, you could change subs to a pair with built in eq or parametric or add an outboard dsp.  Keep the crossover for the mains, run the subs from the second output on your preamp (or y connector if none). I would try the above first.  

Though using a line out converter might work, it seems like another thing in the way of the music. And, I don't see how you will be able to focus on a single frequency to adjust.
I would PM Johnny Rutan (audioconnection) and get his take. 
He knows Vandy's inside out and can give  you the best info, period.

BTW, I own the Treo's with a pair of 2wq subs and will probably go with the new Sub 3's soon. I really haven't noticed any room nodes, thankfully.
But, if they are noticeable, why not try some room treatments, adjusting the crossovers or moving the subs around the room, if possible?
Bob

Thanks for that info!

i would also need to get it back up to speaker level to plug into the Vandersteen sub as the onboard amplifier only accepts speaker level input. 

Its called a Line Out Converter. Couple resistors in a simple circuit, typically about a 10k Ohm resistor that drops speaker voltage down to line voltage, and another roughly 1k resistor that provides some load. You could build one yourself like I did for about two bucks. Literally, I think mine was a little less than that. Or you could buy one from Parts Express or a zillion other places for around $10-20. Search for LOC you will see.

Here is the clearest most complete description I could find. This is what I built mine on. http://www.epanorama.net/circuits/speaker_to_line.html