Okay, I'm going to describe in full detail what i did, and you can adjust to make it work for your setup.
I have a 2.2 setup, Output 1 is Left, Output 2 is Right, Output 3 is first sub, output 4 is second sub.
I first began by setting Dirac 1 to output 3 / first sub, and Dirac 2 to output 4 / second sub.
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I ran the (first of many) Dirac calibration, i only measured the centre position that Dirac uses to set the gains and delays, i hit next, i hit generate filter (target curve doesn't matter, we only want the delays).
After the 'calibration' is over, i go back to the miniDSP interface and check the delays and gains here that were generated by Dirac.
Then I copy whatever delays Dirac generated to their respective output in the outputs tab
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my subwoofers were already gain matched before i started, so i did not use the gain adjustments Dirac suggested, as SPL matching is not necessary when you have the two subwoofers gain matched.
gain matching your subwoofers means that if both of your subwoofers would be in identical locations in the room, they would produce the same output / frequency response. SPL matching is matching the average SPL of two subwoofers in two different locations in the room, it's less effective and it's what a digital processor can do.
So now we go to our next step, aligning the left speaker to the 'subwoofer' which is the summation of first subwoofer and second subwoofer.
so after you have manually typed in the delay from the first calibration into its respective output in the outputs tab in the MiniDSP software, we go ahead for calibration number two
Dirac 1 is left speaker / output 1
Dirac 2 is 'subwoofer' / output 3 + output 4
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Similarily, we take the delay that Dirac came up with and we put it in its respective output in the outputs tab in the MiniDSP software.
Again we do a third calibration,
Dirac 1 is right speaker / output 2
Dirac 2 is 'subwoofer' / output 3 + output 4
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After we copy the third and final delay into the outputs, this is a good time for crossovers, if your speakers have meaningful low frequency output above 40Hz, and you would like to keep them running to have more low frequency sources and further smoothen your bass response then there is no need for a crossover.
Now we run THE Dirac calibration, the final and last calibration with the following routing matrix.
View attachment 150794
and voila! subwoofer integration complete!
I will probably make a more comprehensive thread in the future about the optimal target curve and stuff for Dirac, I experimented A LOT and i feel like a lot of people can make use of that as well.