The SR-6009 comes with MultEQ XT. See the chart in this link:
http://www.audyssey.com/technologies/multeq/flavors
It doesn't have the resolution of XT 32, but IME, XT still does a very good job.
As far as the ability to handle dual subs, that is not included in XT 32; however, most manufacturers have seen fit to include SubEQ with XT 32 (Onkyo being the rare exception) - it is like an add-on/plugin for XT 32 (except you cannot add it if your AVR doesn't have it).
Before XT 32 proper starts, SubEQ does two things to allow Audyssey to handle dual subs:
1) Level matches the two subs
2) Time/phase alignment - the distance adjustment.
After that XT 32 treats the dual subs as one sub for all calibrations (just as your XT will when you hook two subs to the SR6009).
Ideally, you could locate the dual subs equidistant from your LP (judging by your photos, it looks like you may be good on this!). Then the phase/time alignment should be very close.
The levels can be matched using an SPL meter and pink noise. If equidistant, it seems reasonable to trust the same model sub to be equal levels if you position the gain knob the same.
So once you get your second sub, level match them. Position them as close to equidistant as your space allows. Then run Audyssey XT.
It is a given that your time/phase/distance will be off by a little bit. Although I like the idea of it being matched, I wouldn't be overly concerned about it, just yet. Three feet at the speed of sound is 2.66 miliseconds. If it was your midrange or high frequencies, I would be much more concerned.
Play some familiar music or HT with
just the sub playing and tell me how much "impact" you hear or how strong the attacks are. Higher frequency sounds to excite our reflexes from the standpoint of timing. Bass gives the soundscape strength and solidity. That said, I have had several subs that made the sound sloppy/muddy. I have to admit bass/subs are somewhat enigmatic for me. When I listen to sub alone, they sound sloppy because there is no apparent "tightness". However, listening to a 2.1 system the sub absolutely makes a difference. I think it is more a matter of room nodes or over-hang from previous sounds masking the higher frequency attack information for the next sound.
Sorry to digress. Back to the task at hand. I hope the better understanding of SubEQ helps you tune your setup a little before running Audyssey XT.
For music, I would definitely set your sub to EQ2:
The reason is EQ1 is tuned to give you a flat response in an anechoic chamber:
The reason is, unless you have a "non-residentially huge" room, you will get substantial room gain. In your not so large room it is a safe bet you will have well over 10dB of room gain by the time you are at 20Hz. Understand that is the avg. across your room, if you happen to be in a node where your LP is, it gets worse! Audyssey is not capable of suppressing such a huge bloom in bass (I have seen numbers like 8 to 10dB thrown around as max adjustment capability for Audyssey - but have never seen anything "official" on this).
It is a safe bet that the EQ2 curve, after room gain, provides a much flatter "net" frequency response!
You should go ahead and try this if you are currently using the EQ1 curve.
We get trapped into the rut of thinking we want a flat FR curve - well, we do, but that curve needs to be for in our room. For non-bass speakers, anechoic is a fair measure, but for bass, anechoic flat response is not going to be flat when you get it in your home.
So, to your main question, "Hold your horses" and see what you get out of what you've got before spending any more money. If you are discontent with it, I would go the REW measurement approach and post your results along with room layout for the experts here and on AVS to evaluate before springing for DSP mini or anti-mode. Audyssey XT is no slouch; it may be room treatment (or rethinking sub locations) is a better solution. If your room has nulls, pumping more watts into (EQ'ing) them only increases the magnitude of the null while putting an insane demand on your amplifier.
Hope this helps you!