EPP measurements are done by the length of the sides. So, if you're wanting a 3 inch finished hexie you'd use 3 inch paper hexies with the fabric cut a little larger-I usually add 1/4 inch-to fold over. If you're wanting 3 inch finished hexies measured some other way-say side to side-I'd suggest going here to see what size prints up the size you're looking for.
http://incompetech.com/graphpaper/trianglehex.html