Doesn't the parade mode get engaged if at a stop you roll the throttle back after full off, check your throttle without the bike running, you should find that there is small amount of roll back from its normal off position. I thought this was to engage the parade mode. If you come up to a stop and don't roll the throttle back to this parade mode position I don't think the engine will go into parade mode unless the engine is too hot.
The system has to either be enabled or disabled using the method posted by Screamin and sblair; key on, engine off, roll throttle back, etc. Once enabled, the system is automatic and doesn't require any input from the rider. It looks for a cylinder head temp above the threshhold, no throttle, no vehicle speed, clutch disengaged or trans in neutral. When those conditions are all met, the ECM shuts off the rear cylinder injector.
From what I've heard, many folks who just try to ride away normally after the system engages suffer from stumbles or even stalls due to the lag before the rear cylinder starts firing again. Blipping the throttle before releasing the clutch should solve that little quirk by causing the rear cylinder to start firing right away.
As for damaging the crank or the rest of the engine, I wouldn't worry about that. If your crank is so poorly put together that idling on one cylinder could cause it to scissor, your engine won't be running long enough to get hot enough to go into parade mode.
Jerry