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have a few questions as to the best way to take the measurements
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I would certainly forget about the 'other' speakers until I had found the best spot for the two subs.
If you have them in different positions, presumably this is to produce an overall response at the listening area that neither single position provided.
Alternatively, if you've found a single position in the room that provides a fairly smooth response, then I would co-locate the two subs.
Once you've found the best position(s) for the two, then it's really a bit of trial and error when equalizing. In the end, the two subs are acting as a single unit, but you may have to measure each at the same time and offer each a bit of equalization to end up with the two creating an overall satisfying result.
You can certainly measure and equalize for a single listening position, but if you have more than one person listening, it's best to spread out the measures to a bit of a wider area and average the equalization.
brucek