OK....This is what I know feel I know about the proper work flow to get the most out of MCAAC after reading the receiver manual and the Advanvced MCAAC manual. This is also the work flow I plan to use this weekend when the wife gives me a few hours alone in the house.

Work Flow:
1) Set Reciever to MCAAC preset 1 (M1). Now Run
Auto MCAAC with mic in you listening position (I taped the mic to the top of a two foot long shoe horn, and stuck the shoe horn inbetween the couch cushions, so the mic is right where my ears are during listening).
2) Go into
Manual Sp Setup and change the
SP settings if neccessary(crossover to 100hz for me and speakers to small)
3) Now re-run
Auto MCAAC but select custom, and then select
Keep SP settings.
4) Now you have an Auto MCAAC calibration saved to M1 (....note: you must select which preset you want Auto MCAAC to save calibration data to before you enter the audio setup menu.) Now go into
Data Management--------> Data Copy and copy M1's data to M2 and also to M3. Now you have carbon copies of this calibration in M1-M3.
5) Now go into
Manual MCAAC--->EQ Professional------>Reverb Measurement and get a reading on the the frequency response characteristics of your room. Be sure to select
EQ OFF(standing waves not controlled for via MCAAC fliters) in the
Reverb Measurement menu because you don't want the standing wave adjustements (EQ on) to be factored in to the room reverb measurments. Also make sure you haven't moved the mic.
6) After test tones are done, go into
Manual MCAAC--->EQ Professional------>Reverb View , and you can analyze the frequency response of individual channels at various frequencies. Based upon that data, you would select the appropriate capture delay time for MCAAC to capture data during for the upcoming EQ calibration.
Change that time frame under
Manual MCAAC--->EQ Professional------>Advanced EQ Setup to whatever you decide is the appropriate capture delay time ....(
Pioneer recommends 30-50 ms, but they encourage you to analyze the data under reverb view first and refer to the advanced MCAAc software manual for analysis purposes). Note: the default capture delay time is than 80-160 ms.
7) Change to MCAAC preset 2 (M2) before you run the new advanced EQ calibration with the new capture time. Go under
Manual MCAAC--->EQ Professional------>Advanced EQ Setup to start the advanced EQ calibration, and MCAAC should make a more accurate calibration since it will now capture sonic information sooner after the speakers output sound, and get a read on what the frequency response is of the speakers themselves, and not the speakers and all the reverb which accumulates as time passes. (Default capture time is 80-160 ms and thus collects more reverb and less true speaker reading)
Now you should have an accurate calibration. Also, now you can easily compare the Auto MCAAC EQ effects that are stored in M1 with the advanced EQ effects in M2 while listening to content with a simple button press on the remote. You could also juice the base a few db in M3, and also compare running the base a bit hot to a flat calibration that you have in M1 and M2.
Advanced MCAAC Manual (especially read pages 18-20)VSX-1018 owners manual (especially read pages 38-50)
If I am wrong about something (which is possible), let me know. I did this so that folks looking to get the most out of their equipment could better do that. The whole Auto MCAAC thing can be a bit confusing, so maybe you can benefit from my research and tinkering.