TOPIC:

I have 3 subwoofers.  I used REW to align the first 2 subs, I adjusted the delay and phase until they both produced the best output, then proceeded to add the 3rd subwoofer, made sure the phase matched, then adjusted the delay until I got the best output out of the 3 combined with the least dips.  After all that I ran EQ with a house curve and applied the filter generated under PEQ, but that was a mistake?  I later ran Dirac Live on my receiver which would then apply another filter on top of what PEQ is doing, is that bad? Do I need to remove PEQ, stop at the sub alignment with REW and run Dirac Live and let that create it's own filter?

I've learnt a bit more since originally asking this question and added a second sub a long time ago so not sure how long ago this thread started.. Shame there aren't dates on these things!

So assumption is your AVR has a single LFE out that goes to the minidsp so dirac doesn't see multiple subs, but only their combined output. The norm would be to set individual PEQs on each sub via the dsp output channels before running dirac. Note this is individual PEQs dedicated to a particular sub if you applied a 'global' PEQ to all of them then that might not be advisable.

Have you looked at the minidsp tutorial on using MSO (multi-sub optimiser)? It's exactly what MSO does - takes measurements from each individual sub, works out best delays and crossovers and levels for you and creates as many individual PEQs as you allow. You do all that before running Dirac. Results can be spectacular. 

That is correct, my receiver has just one subwoofer out which is going to the MiniDSP.  I have not seen the MSO tutorial, appreciate the suggestion, I will check it out