You should have a read of my thread about 749 with Power Commander 3, just recently fitted.
PC3 fitted to 749 Bottom line is I had it set up on a dyno and it wasn't very good. Subsequent tweaking on the dyno didn't help it. Ended up using the map supplied for the asymetric Termi and it seems fine on the limited test I did today. The advantages I found of the PC3 over the Ducati ECU that came with the Termi was that it the throttle seems now much more responsive. Small changes in throttle position can be felt so it feels much better to ride. Might be wrong, or wishful thinking on my part, but that is how it seems.
You ought to check that there is a map to suit your bike/exhaust though otherwise setting up on a dyno will be the only option.
Ducati maps