Both USAF and USN pilots have tremendous leeway in flying their missions.  They do all their own mission planning and have all sorts of individual laptop computer programs to assist them in that.  And once the mission is planned, they have tremendous latitude in executing the mission and can modify the plan pretty much at will to accomodate unplanned events caused by things like weather and/or enemy action.  Its their butt in the seat and they get to make LOTS of choices.  In fact, they are expected to.  That's why all USAF and USN pilots are commissioned officers with college degrees.  They are expected and required to be able to think for themselves.  That's when flying operationally.  And they train the same way they are expected to fight.

As for flying by the "handbook", that's pretty much a given.  USAF calls their flight manual a "dash 1" and USN calls it a "NATOPS" manual.  Military aircraft are very complex critters.  You want to operate them by the book if you want to stay alive and healthy.  That being said, there is lots and lots and lots of freeedom beyond the details of the flight manual.

There's an IMAX movie out called "Fighter Pilot - Operation Red Flag".  It's a little staged and Hollywoodized, but in many many ways VERY accurate.  Go watch it.  It'll provide a many insights.