Pain above the kneecap usually means saddle too low. While sitting on the saddle normally, either on the trainer or leaning against something, unclip one foot. With the heel of that foot on the pedal, back pedal slowly until at the bottom of the stoke, your crankarm is aligned with the seat tube. Your heel should just barely be in contact with the pedal with your knee completely locked and your pelvis level. If your heel is firmly in contact with the pedal, raise the saddle. Some people leave a 4mm gap between the heel and pedal. Try this with both legs as they may be different lengths. Your sore knee may be on the long leg.

Once you have established saddle height by this method, *then* you can experiment with adjusting the precise saddle height by mm. With modern pedals, float is seldom the problem, nor is pedal size if you are using good quality cycling shoes with very stiff soles.