Window sills are kind of hard to explain without pictures -
#1. The window sill gets installed before the window trim molding.
To make a sill, measure a piece of wood (whatever you're making the sill out of) to be the width of the window PLUS the width of the vertical molding that you're going to put around the window - and optionally - PLUS 1 inch so the sill ends up extending 1/2 inch (on both sides) past the window "picture frame" molding.
Then, you need to notch it at each end so that it fits into the window frame (inside the sashes.) Again, this is difficult to explain without pictures, but it should be faily obvious when you put a length of wood in front of an untrimmed window, that you'll have to cut away at each end to make it fit.
After it's cut to fit and installed, you install the rest of the window molding.
I know that's not a lot of help - but it's easier done than said.