Speakers will always look different from each other in a room in the frequency response. Exact mic placement is necessary in order to measure both speakers at once, but it seems to be tricky to set this up perfectly. Usually, the easiest way to measure is to measure each speaker individually for ETC measurements and frequency response. If you want, you can always average the two graphs to get a picture of total freq response at the listening position. To show bass response and modal activity, using both speakers is helpful to drive more room modes (in other words, show modal ringing better in waterfall graphs in the sub 400hz range). To test SBIR, you will want to measure each speaker individually.
In this thread I posed some questions about testing. I didn't receive all the answers I was looking for but got a couple good responses none the less. Perhaps it will be helpful to you: Verify my testing procedure
To sum up, different ways to measure show different types of results. If you are trying to figure out speaker placement by viewing SBIR, you should be looking at certain ms ranges while measuring one speaker at a time. If you have a comb filtering reflection coming from somewhere, test each speaker at a time and look at the ETC. Find out the distance by the time the reflection reached the mic, and see if its possible that distance is where the comb filtering is coming from. If you are looking to see how much your traps have affected modal activity, a single speaker or subwoofer in a tricorner in your room with a mic in the opposite tricorner will show modal activity best. If you just want to show measurements in listening position, my first paragraph has the easiest way to test this. Test speakers individually, average the responses. For sub 400hz waterfalls, test with both speakers on.