post about how to get your saddle height right on your road bike in order to optimise your pedal stroke. Another check you should consider making is whether your saddle is in the right fore and aft position relevant to your pedals.
To check this, you'll need a wall and a plumbline. Put your pedals in the quarter to three position and using the knee that is furthest forward, drop a plumbline from the knobbly bit on the side of your knee down. The plumbline should go exactly through the centre point of your pedal axle.
If it doesn't, simply loosen off your saddle and adjust backwards and forewards until it does. It will only take you a couple of minutes to check, by making this adjustment you can ensure that your power is going right through the pedal.
When you've done this, it may change your cockpit position forward or back, if it feels different then you should take note of how far backwards or forwards you have adjusted the seat and then change your stem accordingly by either shortening or lengthening.
When bike fitting, by doing this measurement of height and fore/aft, it then determines the correct stem length. If you want a lower position on the bike, go long, if you prefer a more upright position on the hoods - go shorter.
If you have a look at the picture above of Nicole Cooke, you'll see that straight line down. As always, if you want to get really serious, consult a bike fitting professional.