Use a scraper to get of the heavy flaking old paint. Use a wirebrush and sandpaper as already stated by you to remove other flaking paint. Brush off all dust and particles. For a good seal to reduce the possibility of flaking occuring again. Apply a stabilising solution like the one here [broken link removed]
Then apply the paint on top of this solution when dry. For a long lasting finish, apply a minimum of 3 coats. Don't worry about the old paint, there is no need to take it all off. As long as you have prepared the surface like mentioned in first paragraph all will be fine. If all of your sills are flaking. Id definitely recommend applying the stabilising solution. Its a godsend for old worn window sills.