[aerohead]

After glassing,I have sabre-sawed a line at the outside perimeter of where the glazing will be,then slid the loose section in (like a drawer) until its depth is a little deeper than the glazing itself.Then re-glassed this loose section like a patch to bond it,forming a nice landing zone for the glazing.Then,cutting out the smaller area which will actually be the visual opening.
Short of having a mold with joggles formed in,it's a quick and dirty way to end up with flush fitting components.
Blacking out the inside of the glazing perimeter gives a nice OEM look.