The Power Commander lets you adjust/offset the main fuel tables in the ECU. However, when you are cruising along and suddenly grab a fistful of throttle, the engine wants more fuel than it did just a moment before (at steady state loads). The MAP sensor detects a drop in manifold pressure and tells the ECU to add more fuel for acceleration.
The link I posted above gives you the ability to tell the ECU to add more or less fuel when you suddenly accelerate from low engine speeds. This can be used to improve throttle response and/or to improve cruise mileage. Most PCIII owners (and even many tuners) don't know that this application even exists, or how to use it for different things.
What this means is that you can tune the throttle position/engine speeds at idle and where you cruise much leaner, and still have the ECU add enough fuel to get good acceleration. Most bike engines today will run very well (and very safely) at low loads (cruising) when tuned very lean (as lean as 26:1 AFR). The manufacturers can't do this because it raises the total hydrocarbon and NOx emissions, but there is no reason why you can't have your cake (performance) and eat it too (with improved fuel consumption).
[And doing this keeps the pipe tips and sparkplugs from becoming black with soot.]
Clear as mud now, right?
I can add a good bit more details, but it is easy for you to tune for lean-cruise if you know how. Another thread would be a better place to go into details.