Bi-Amp Calibration assistance/advise

I have a set of NHT 3.3 speakers. I use a dedicated NHT SA2 Subwoofer amplifier for each speakers bottom driver.  The upper end of the audio spectrum is then connected from the SA2 to a Tube Amplifier to drive the top end of the speaker.

This Sub amplifier gives me great flexibility to configure for my room/system. I am looking for some suggestions on how to best calibrate these speakers with this amp.  

Here are the directions from NHT I have followed (Method #1, recommended):

Your advice is appreciated.  I am trying to make sure what is happening in my room, is optimal!

Jeff in Detroit
If you followed directions, you're good to go. I would make sure the speakers are in their best position...move them around the room until it sounds best to you.  The subs should be almost inaudible.  You don't want a juke box.