Richard:

I am not a professional painter (and I would never paint an airplane again), but here is what I did.

The panels are all painted in advance, while supported on small pieces of wood so that all the edges are painted.
Since my paint is very heavy (polyurethane),  I do not paint any place that is not visible.  That means the flanges under the panels are not painted.  I  add multiple layers of masking tape on the flange to approximate the thickness of the panel.  Masking tape is cheap but applying it is very time consuming.  see note above in parenthesis.  This is not always perfect and in some cases, I have had to sand the sides of a panel to get it to fit into the opening.

The screw opening in the panels are another problem because the paints tends to build up there.  I have enlarged the openings slightly to allow for this  but that is not always the answer.  I have considered putting screws in the openings before I paint the panels but I think that the paint would tend to fill up the opening and getting the screws out could be a problem.  So I just paint my panels and ignore the openings.  Then, if the screws dont seat properly, I touch the screw opening in the panel with a reamer to remove some of the paint and try again.

If there is ever a next time, I would have my plane professionally painted   Good Luck

Bill Hogarty.