You can use time acceleration, but limit it to a sensible 10X--50X depending on how fast your computer is. (you can set this under Extra->Vessel Configuration->Project Apollo Configuration, in the Orbiter Launch Pad)
Always make sure your attitude controls in both the LEM and CSM are set to "free" for time acceleration above 1X. You won't use it nearly as much as a normal orbiter addon, as the checklists will keep you quite busy.