They say you shouldn't do more than 1/3 of a plant at one time.. So you can top and prune.. I like to prune from the bottom, while others like to top them..
Both is a bit different.. but with a time in between, you'll be fine.
So you'll top now, which will cause the bottom to bush out.. then in a week you trim the bottom 1/3 off and throw it in flower room.. clean it up again after a week or two of flowering..