The most common mistake that people make when flooring an insulated attic is squishing the insulation. Attic insulation works because it traps air. Compress that insulation under a floor and the air gets pressed out, robbing the insulation of it's efficiency.
In a perfect world, you'd buy insulation just thick enough to fit inside ceiling joists, floor over and be done. But, here is the kicker. Most ceiling joists are simply not deep enough to hold the 12" to 18" of insulation required by today's energy standards.
I suggest you only floor that portion of the attic you absolutely need for storage. For the rest, install 12" to 18" of insulation and let it rise above the thickness of the joists. Also, be sure to use unfaced fiberglass batts, and make sure you have enough attic ventilation to avoid moisture build-up.