When drilling fiberglass it is always recommended to use a "brad point" drill. Here is an example:
The brad point holds the drill in place, then the outer edge cuts the diameter from the outside in. A standard drill cuts the center and tries to screw the drill into the work, which can shred the work and chip out large sections of the gel coat.
Since you need a rectangular hole I would use the drill twice, once at the top and again at the bottom of the rectangle. Then use a hacksaw blade to cut between the two holes and square up the ends.