Until Dirac Bass Control arrives to MiniDSP, you need to integrate the subwoofer with the main speakers before any interaction with Dirac Live.
You must integrate the subwoofer by placing it in the best possible location to avoid cancellations or to complement the cancellations from the main speakers that you cannot avoid.
Once you have placed the sub in the best spot, you have to integrate it in terms of volume and phase with the speakers. That requires establishing the crossover point (for the sub and, if you wish, for the speakers).
My advice is to do all of this in REW. It is a manual process that Dirac should theoretically handle, but ultimately you learn to do it quickly and well. I even recommend generating the PEQ in biquads from REW and importing them into MiniDSP.
Personally, I prefer not to touch the speakers at all and apply all PEQ to the subs, as they are usually the ones with room mode issues.
With the sub well-integrated, you can then open Dirac and perform all the measurements.
Dirac will recommend an automatic curve. I do not recommend it. It tries to be too perfect and alters the sound significantly. I prefer to replicate the average curve between the left and right channels and prevent Dirac from trying to fill dips. However, you can use Dirac to smooth out some peaks above the baseline.
When exporting, I recommend testing two alternatives: exporting with gain/delay enabled and exporting to another preset with gain/delay disabled. When I used the UMIK-1 microphone, I preferred gain/delay disabled; now that I use the UMIK-2, I prefer leaving it at the default (enabled).
On the other hand, although Dirac recommends different curtains, I would discard any correction in Dirac below 60Hz and above 800Hz. Move the curtains to that spectrum. Below 60Hz, it tends to want to fill dips and generates delays that ruin the bass, and above 800Hz, it can force a very metallic and unnatural sound.
You might ask yourself… why do I want Dirac if I had to go through a complex manual process beforehand? Because Dirac does one thing very well that is much more complicated with REW: it adjusts phases across the frequency curve and achieves a much more precise sound.
But be careful, as it is highly dependent on the precision of the microphone and the precision of the measurement positions. If you measure the center, then 40cm to the right, and then 70cm to the left, it will shift the image to the left. Try to ensure that any movement away from the center is exactly symmetrical relative to it. The main measurement is very important, but other measurements affect the soundstage.