RTA measuring with DEQ

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I built my subs according to Linkwitz's specs on the Phoenix dipole design. With the ECM8000 and the deq, measurement on the dipole subs alone is flat from 40hz- about 200hz.
When I rta the MTM from 80hz-20khz, there seems to be some interactions between the MTM and the subs, how would i go about it?
Mute the subs when I rta the MTM (mic at tweeter's level), then use the results to measure the subs (now muting the mtm and mic at sub's level)?

Keep in mind that I measure the MTM about 1 meter away and at tweeter's level. The subs were measure about 1-1.5meter away and only a few inches from the floor.

How do you guys get the best out of your rta?
 
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