Setting saddle height should be independent of what sort of pedals or clips you are using. Photos or caculators and tape measure are contraindicated. This is how you do it: With the bike next to a wall or some sort of handhold, mount the bike while wearing your normal cycling shoes. Get in your normal pedaling position. Put your heel on one pedal and rotate the pedals so the pedal with your heel is down and aligned with the seat tube. You heel should just barely touch the pedal with your knee locked and your hips not rocking. Some people like a gap of up to 4mm. No more. Adjust saddle height until this is true. You may have to rotate the pedals a couple more times to make sure you haven't rocked your hips. Now try it with the other foot. Your legs may be different lengths. I set my saddle height by my shorter leg.
Once you've done this, you'll pedal correctly, no matter what sort of pedals you have. As it has been said, if you're using toe clips, you may have to space them out to get the ball of your foot over the pedal spindle. Clipless pedals of course resolve these issues very simply.