just gently sand the filler down to the existing surface but don't sand into the surface.
The gelcoat is the white (typically) surface over the dark green or brown fiberglass, I'm guessing about 1/16" thick? But that's the skin of the boat. Water will wick into the underlying material.
Once you put a filler like marine tex on stress cracks, the cosmetics of the boat are no longer an issue. Are you going to paint it where you patched?