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.
Note that the AGC is the prime factor in determining max safe time acceleration. The AGC takes quite some time per timestep to operate so having it running with time accel. will slow down the simulation. If you want to speed up even more you can put it into standby and pull the breakers. You will however need to do a time and state vector update afterwards.