Hi Glenn,
Thanks for your enquiry. I am pleased to advise that a new feature is scheduled for delivery in Version 6.2 where the hole is automatically added into a flat ceiling when adding a skylight or roof lantern, effectively working in the same way as is the case for doors and windows on walls. This version will be made available in early to mid-May.
In the meantime, the recommended approach is to simulate this by not adding a ceiling, placing the item and then surrounding it with graphic boxes to represent the ceiling around it.
If you need any further advice, feel free to contact the Fusion Support Team.