Here is what I did to setup my 5A's:
1. Place them for the best sound possible (imaging, sound stage, timbre, etc...) with the subs off
2. Using test tones and some type of measurement device (I used a Velodyne SMS-1), measure one speaker at a time
3. Try to use the 11 band equalizer to bring down peaks and only add a little to dips
4. Once both speakers have been measured and set, measure with both speakers playing
5. Make adjustments based on both speakers playing
6. Listen, listen, listen!!! Listen to some good upright bass, percussion, etc...you want it sound natural and have the right amount of slam, speed, and detail.
This process took multiple hours and multiple sessions before I finally left things alone. Don't rush it. Also, don't worry if things are perfectly flat. At the end of the day, go with what sounds best to you and that you enjoy.
Best of luck.
George