When ever possible, I avoid putting a hole in the roof.
Is your roof gable or hip style?
http://www.texasinspectionpartners.c...mages/0407.JPG
If gable style, consider using a wall or eave mount.
http://www.3starinc.com/antenna_wall_mounts.html Drilling through the wall of a gable, and then sealing with outdoor caulking would be preferable to a roof deck penetration. Use a
drip loop to prevent water from draining directly to the caulked hole.
If you have no choice but to penetrate the roof deck, you'll want to use conduit, flashing and a weather-head that are appropriate for your roof construction. You may want to consult with someone who has experience with roofing installation and repair to be sure you're not overlooking something important.