Got my Flex in yesterday for my desktop setup, a few days earlier than initially expected! Dug up my old home theater sub and shoved it in the corner then spent a little bit of time figuring out how to make all the pieces work together.
Things came together when I reset the Flex to default configuration, disabled Dirac (I had run several Dirac scans already) and followed this general outline.
1: Run a L+R scans with my XO in place and sub off
2: Run a scan of the Sub, with my XO in place and the speakers off
3: Work up a PEQ filter for the sub in REW that looks nice and flat
4: Turn on L+R and subs and run a scan to see how the volume between the sub and speakers match up
5: Turn up the volume knob on the sub until the general volume levels match up closely between the speakers and sub to the house curve
6: Run Dirac and feed it my house curve.
I'm going to work on tuning the sub PEQ a little bit more to flatten it out but as of now I'm pretty happy with the results. This is a really neat little device with a lot of power and flexibility!