You don't say whether the sill is made of wood or plastic...
I would use a filler called "Davids Isopon" or similar "Two Part" filler
It's hard to explain without drawings, but I'd get prepaired by getting a piece of smooth wood , or similar material, which covers the legnth of damaged sill...a piece of silver foil the same size ( to stop the filler sticking to the smooth piece of wood)
Mix up the filler, put enough in the damaged hole to fill it, place the foil on top then get the smooth piece of wood and place this on top of the foil , Use a "G" clamp or similar to gently squeeze out superfluous filler. That is as long as you can get to both sides of the dammaged sill..... This you should leave till the fillers gone hard... When you remove the clamp, wood, and foil the filler should be easier to sand down to a smooth finish .
CHUM
Chumley, October 2009