Answer:
Cut-in should technically be done prior to rolling the walls and ceilings because you want to keep a "wet edge" so when all of the paint dries, it blends together.
But if you are using a flat paint, this rule is less strict and you can usually get away with doing the cut-in at any point.
If after cutting-in (and allowing the paint to dry) you find that you still see the cut-in lines, (and assuming you are using flat paint). Cut-in a second time. The amount of paint on your brush is less than your roller, and cut-in often requires two coats. You will want to "feather -in" the cut-in line into your wall (or ceiling), i.e., dip your brush in your bucket and using the edge of the brush pushed into the cut-in line, apply your paint and drag it along the edge of your line, as your brush releases the paint, stroke the nearly dry brush into the wall or ceiling that you are trying to blend into, this is "feathering."
If you are cutting-in with an enamel paint you will probably have to cut-in (do it twice, waiting between coats to let the first dry well) and before the second coat has dried, re-roll the wall, bringing your roller up into the cut-in line.