Another way to establish saddle height is to take your standover height (inseam) and use the formula: inseam (cm) x .883 The resulting measurement will indicate the distance between the centre of the bottom bracket spindle and top/middle of saddle. Should get you within a cm of ideal.
Obtain your inseam by standing with feet 6" apart in stocking feet. Press a hard spine book against your crotch (pressure like saddle), and using the end as a square, make a mark on a wall at the top of the book spine. Measure from floor to mark. This measurement will also aid in choosing your road bike.
Pain at the top of patella almost always indicates a saddle too low.
Do you use clipless peddles? With or without, your foot may be positioned incorrectly on the pedal.
As others have said, keep gearing low.
More tips @ VeloWeb.