Um , maybe bad news coming. Did you prepsol (wax and grease remover) the area before applying the primer? If not you risk problems in future, and your choices now are to remove the primer (sand back and/or strip with thinners) and prepsol it properly, or press on and see what happens later. It might be alright, or you might have to do a lot more work to fix it up.
Prepsol is necessary to clean wax and grease and especially silicone, which will cause fisheyes (little craters with visible rings) or other imperfections in the finish. Be very thorough if you've used polishes on car. Sanding first as below will help if you have.
No need to sand for a key and doing so might give poor base which will mar finish, but a clean with 1200 or preferably 1500 (you'll get 1500 at decent paint / auto paint stores but 1200 is best most hardware stores seem to carry) wet and dry is good. Get a bucket with a bit of plain soap or dish detergent and sponge it onto area you're working on to keep it lightly lubricated and remove debris while you're sanding. Wrap sandpaper around another firm small sponge (common kitchen ones about postcard size and quarter/half inch thick) to get flat contact with sill and follow contour. Prepsol after sanding.
Make sure filler is sanded right down flat and feathered on edges where it joins paint. Run your flat hand (not just fingers) over it while sanding to check. If you can feel any lines or bumps, they'll show in the finish, maybe a lot more than you'd expect. Finish filler with 1200 wet and dry same way as above.
Be sure to prepsol the whole area to be painted before applying the paint. Give it two or three goes, using a fresh clean cloth each time, rubbing firmly to get stuff off, and wiping dry with a different fresh clean cloth. Make sure primer is fully dry from prepsol before painting. Tack rag before paint coats is recommened to remove all dust, but I've never done it and no problems to date.
When spraying, do light coats. Don't expect first coat to cover fully. If you can still see primer through it it's ok. Build up several coats of same density. You can usually recoat after 5 or 10 minutes, or whenever it's dry. Trying to put thick coats on will cause runs and sags. Half a dozen light coats is better than two or three heavy ones.
Overlap each spray line and keep working in wet paint. Spray can paint dries quickly and as you're doing a long narrow strip might be better to break it into three or four short sections to stop running into dry paint when you get back to start.
Just a hint on masking tape, from someone who found out the hard way. Get proper auto masking tape and be careful pulling it off - it's a real bastard when you pull off chunks of paint with the tape.