The quote from the Nissan tuning guide fits my earlier comment. Basically, you are balancing fuel, spark, actual measured air mass and theoretical VE derived from forumulas based on the known displacement of the engine, RPM, and thottle position (really, VVEL).
There's probably limits to how great those values can be before they are not doing a good job of modeling the physical reality of acutal air mass ingested at a given RPM and VVEL position(s).
Modeling airflow is a real PITA, and yeah, a lot of it is trial and error, especially if the values you can record/ adjust aren't intuitve.
I guess you can try datalogging VVEL and MAF g/sec (assuming you can get this data from either upRev or from an OBDII scan tool) and try to figure out more precisely what the range of values ought to be.
Actually -- let me recommend a really good text that may be helpful as you learn how to tune it -->
Amazon.com: Engine Management: Advanced Tuning (9781932494426): Greg Banish: Books
I found that book to be incredibly valuable in figuring things out when I used to tune my previous car.