First, unless you have extremely short legs and very long crank arms there is no way your thigh would be parallel at the top of the stroke in any normal saddle position. Google bicycle fit and you will find plenty of guidance, but basically you should have a slight bend in your knee when at the bottom of the stroke with your foot properly positioned on the pedal (ball of foot). Some recommend putting your heel on the pedal (other leg hanging free) and adjusting so that your legs are straight and hips level. Then you adjust as needed from there.

The saddle is adjusted to the pedals, not to the ground. When you start or come to a stop it is correct to be off the saddle standing between saddle and bars. It is also somewhat important to have a good fore-aft position for the saddle. More info would be helpful - frame size (center of crank axle to center of top tube), leg length (floor to crotch, no shoes) and crank arm length (usually written on inside of crank arm (165/170/175, etc.)