if this program does not require taking many measurements at different positions like Odyssey, then i think the only place you should put the microphone is exactly where your ears will be doing the listening (middle of the head).
it seems logical to me, as the sound will then be equalized where you do your listening, not in a spot where it will not do anything positive to your listening spot.
doing it in the middle of the room will most probably make it worse at your listening spot.
dips and peaks change all the time when one moves around in a room; if you want to hear what it does, send a 1 or 2 kHz tone through one speaker and then slowly walk around in the room while listening to the tone. you'll be surprised.

to be sure, try both and listen for a couple of days before you decide which is the better one.