Cover page = the card-stock cover you put your script in, three-hole punched, brass brads in the top and bottom holes (middle is left empty). Your cover should be white (I used to buy scripts from a script service who sent them in a light-blue card stock, but understand it's not the norm) and completely blank, nothing on the front or back.
Again, the reader/exec/producer/etc. will more than likely write the title on the spine of the script; that way as they go down their stack of scripts, or along their rack of scripts, the titles are plain to see.
Fly page: I've never heard this term used before. I'm thinking, however, that it's the same as a "splash" page, which itself is for the most part the first page (of your script -- not the title page).
If anyone can correct me on the fly page, thing, though, please feel free.
