This question is probably for you gonk as I know you are using the Velodyne system for bass equalization. After having ignored my R-DES (Onix bass equalization system) for a few month I decided it's time to give this a try:
The manual states that all full range speakers should be disconnected before running the test CD with sinus frequncies ranging from 16 to 120 Hz. So to run the test I did not change the settings in the 990 menue and simply turned off the M2200 that power the speaker. I set the gain control on the sub (PBS12/+2) to ~60% and either set the crossover control to disables or enabled with the crossover frequency set to 150 Hz. I used a digital Radio Shak SPL meter set to slow response and C-weighting.

In general I just want to know if this is the correct way to do this?

The curves show a response ~85dB (some dips and spikes) but then fall off rapidly above 80 Hz and drop to ~63dB at 106 - 120 Hz. (Pink noise SPL was set to 74 dB prior to bass frequency intensity recording.)

Please let me know if this sounds strange to or if I missed a significant point in he set up. Thanks!

I've read a number of R-DES threads at AV123 but haven't messed with one. The specific process is pretty different from the SMS-1. Without hunting down the R-DES manual, I can offer a couple thoughts... Are the frequecy sweeps played with a CD? If so, that explains your results. The 990's front channel crossover is set to 80Hz, and with the fronts disabled the sub is on its own. With no LFE track (since it's a CD we're talking pure stereo with just the 990's bass management to provide a signal to the sub), the sub will be active below the crossover point - clearly set to 80hz in your case - and once you cross that point it'll drop fairly rapidly. That should be OK, since you're going to be focusing most of your attention below that crossover point anyway. I suppose that if you were able to get any dips and spikes resolved in that sub-80Hz range and still had an EQ channel or two unused, you could bump the front crossover up to 120Hz or 150Hz and check for fluctuations between 80Hz and 120Hz - the sub would only operate in that range with LFE track material, but it could still see use from time to time. Once you were done, you could set the front crossover back to 80Hz.

One thought occurs to me that may contradict the R-DES instructions. I like having the front speakers on along with the sub when using the SMS-1 because it's a very effective way to achieve an accurate and uniform calibration of sub level relative to the mains. All you have to do is adjust the sub trim (at the sub's amp, in the processor, or at the sub EQ if it offers a volume control) until the average level of the sub (all of that material below the processor's crossover point) is in line with the average level of the front speakers (all of that material above the crossover point). Folks who like their sub a few dB hot or cool can always adjust from that baseline. I don't see why it's necessary to disable the speakers, although I would definitely recommend making sure you are in stereo mode and aren't applying any surround processing.

Thanks for your input. I obviously made a couple of mistakes:

1) I operated the 990 in 5-channel stereo when running the sweep from CD.

2) I had the crossover for the fronts set to 40 Hz and 60 Hz for the center.

I will try your recommended settings (Stereo mode, crossover for mains set to 150 Hz) next weekend.

Questions is if it would be better to diable the front speakers in the 990's menue or simply turn the power amps off?
Also, should I set the front speakers to small or large at this point (main speakers: Onix Rocket RS1000 Sig)?

You were right when assuming that the R-DES manual recommends to take out the full range speakers completely. I will make measurements both ways and see what changes in the frequency response. You can load 4 different equalization curves into the device so that I can switch between different setting and pick the one I like best.

As always your comments are very helpful and appreciated. Thanks gonk!

I don't think that the 990 will let you disable the front speakers. I think it just allows seleting either small or large. I'd definitely set them to small - otherwise the sweep from the CD won't get sent to the sub, since all of the information is in the left and right channels and the 990's bass management has to do the steering.