Once I you have the tune installed, 87, 91 or 93, are the adjustable parameters changes to that tune or changes from stock baseline?

SO what I am wondering is if I have a tune installed and start playing around with WOT spark or WOT fuel settings am I adding to what the tune has already changed or ...

Is it safe to say that if you run a tune to high for the octane gas you are running the engine will knock and timing will be retarded by the PCM? So if I load the 93 octane tune and use the data logging to record a couple WOT runs and I get no Knock retard then I should be OK running the 93 octane ...

Where do I find good desriptions of what all the adjustment do? Like WOT fuel or Spark ect. Would realy like to know how to use my tuner correctly. Not just make changes and see what happens. Is there a write up or PDF I can download and read?

Thanks

Jake