Sounds like you have lousy sills which you should ideally replace
(particularly if they don't have a drip groove on the underside).
If you prefer to modify the existing, you need to get a flat surface,
preferably sloping away a fraction. Polyfilla Exterior filler is fairly easy
to use as a skim although I would use car body filler if you can face the
extra work. Then you need to get something genuinely waterproof on there.
Pliolite paint is good but any solvent based paint will be better than
conventional masonry paint, which is not at all waterproof IME.