For a multiplane roof:
Clicking on the eaves and using Add or Subtract from the pet palette will allow you to make a hole in the roof.
Clicking on the pivot line and using Add or Subtract will generate new ridges.
Generally when the roof is selected, and the roof tool is active drawing over the selection usually creates a hole - except in the case of a multiplane roof with 0mm eaves. So we are investigating this anomaly.
James Badcock
Graphisoft Senior Product Manager