TOPIC:

While performing a Dirac Live calibration, all other processing must be turned off. In particular, be sure to turn
off:
 Up-mixing such as surround-sound simulators
 Surround decoders such as Dolby Pro Logic
 “Effects” such as hall or ambience simulators

So from this info should my MARANTZ 6009 be set to STEREO output ? Obviously w Audessy correction turned off...

No, you still want multichannel audio going through it, what you don't want is the AVR moving signal between channels.

(OK, except for bass management.)

so is AUTO decode the best setting for the MARANTZ ?

From the manual, it looks like Direct or Pure Direct would be best.