Does anyone know if adding empacman will cause problems?

Only if you place it on the /drive0 partition and have it run from that location all the time.

Since Drive0 is the music partition, if you run any application from that place, then you will get a failed synch each time you try to synch while it's running.

I solve this problem by only running my third party apps in @DC mode so that they only appear when I'm in the car. Since I only do synchs on AC power, the apps never interfere.