First of all I cut the rough neck with a bandsaw (and headstock angle too).
Then I rout the truss-rod channel when the sides are still square, then again I cut the sides. Then I cut the fingerboard, and glue it. After the glue has hardened, I start to shape the back of the neck with rasps and sanding paper. Then I radius the fretboard, put the frets on, and paint .
Oh, since I made 3 neck-through guitars, the final shaping of the neck is done with the wings attached... don't know if that's the right way, but works fine for me.