For basic saddle height you put your heel on the pedal at full extension the leg should be perfectly straight, then when you move the ball of your foot back over the pedal axle you have the correct amount of bend in your leg for riding. The knee over the pedal axle is a bit more controversial, however if you have the your pedals at 3 and 9 oclock you drop a line from your knee cap to the forward pedal axle and it is supposed to be in a straight line, this is for fore and aft adjustment of the saddle. FWIW depending on the bike frame size, saddle position and crank arm length this may or may not hold true.

When it comes to fit I am more old school and sit a bit more upright and further back on the bike, comes from years of being a climber and racing back in the 70's. Current bikes are much more aggressive and the rider sits further forward. Different strokes for different folks. For me as long as I am comfortable and reasonable efficient I am not going to worry about a pro fit. I ride multiple bikes and it would be cost prohibitive to have a pro set up on all of them. I was at my LBS a few weeks back and they have a new fit system using lasers, as a joke and to show one of the new employees how the system worked, they had me set up on it with my city bike....

Aaron