Couple of ways:
1. Plan ahead:Record one cycle of silence when comping. Double-click the "silent" take to open the Audio File Editor: Functions>Silence to make sure there's no residual sound. Make selections on this take where you want silence.
2. When using existing takes that don't include an empty/silent take, make a selection where you want silence on a Take that you know you don't plan to use. Double-click on that selection as above.