There is no right or wrong way to do this, but some ways will be easier than others. It really is a lot easier to rout on a flat than a curved surface, so you really want to rout when the body's still flat. Also any holes for posts unless you have a pillar drill/drill press.

Whilst you could do some rough shaping while the two body halves are separate, to get curves on the two halves to match up, they will really need to be joined together for the final shaping.

It is far less important when the cutting out of the body shape occurs, though I'm thinking that a binding channel may be easier to cut with a flat top if there is any binding and it follows a straight line around the edge of the body, rather than follow a more contoured path.