You've got a couple of issues that you will need to be concerned with to put a deck on a roof (I'm currently considering doing the same thing with my covered screen porch).
The first consideration is structural. Sorry to answer a question you haven't asked, but you will have to put down joists, probably cut to a 3/12 pitch, to go over each rafter to distribute the weight evenly, or you will have to put in a header over the outside wall (down near the facia board) and somehow secure that to the roof, or build some kind of sub-roof truss system to distribute the weight of the deck if you only have a few deck-to-roof points of contact.
But to your specific question. There is no good way of sealing holes puched in a roof. Tar and silicone are often used for this, but wrongly so. The holes may seal for a while, but tend to open up again, and often you don't notice the moisture until extensive eater damage has already been done. If you must put the deck wood members on the roof, I would use metal brackets (ones I would probably make myself) to slide up under a shingle tab, where I would use a galvanized #10 (or so) wood screw and roofing tar (under the tab). You want to be careful not to rip the tab as you lift it up to work under it, and heating it up a bit first will help (wear gloves!). Also, I wouldn't run a framing member parallel to the facia board (at 90 degrees to the down line on the roof), as you will have to allow some means for letting water pass through and it will be a collecting point for everything (leaves, needles, etc, etc), making it a moisture holding point. Not good.