There's a thread in the Tuning section of the forum with a how to use it.
First things first, balance your throttle bodies and do a 12 minute tune. The 12 minute tune is this:
Start the bike without touching the throttle. Let it get up to temp so the fan comes on.
Let it idle for 12 minutes or more like that.
Should result in a slightly smoother tune.
For the throttle bodies there are a few how tos, but essentially start the bike and while idling adjust the forward most cylinder so the vacuum is the same as cylinder 2 in the middle then do cylinder 3 to match.
Finally adjust your throttle position sensor to exactly the factory spec, I think it's 0.62 volts If I remember right.
Those should help out the running rough issues. From there, I'd suggest sending
@HansO a PM for a stock bike tune to pep her up.