I've done it both ways. Really doesn't make a lot of difference. However, for the brightest crown dip, I don't stain that area. I stain the lower part of the arrow, then dip the stained area in clear fletch lac (2 coats). Then I dip the crown area in two coats of white (my preferred crown color). For a different crown color, I put one coat of white down first, then two coats of the top color.
I've also stained the entire arrow and then dipped like above as well. Really difficult to tell the difference in color. No difference in durability.