Start with the basics.

First is saddle height. With your heels on the pedals, slowly pedal (easiest to do this pedaling backwards, while holding the bike and yourself upright using a handy wall or doorway). Your legs should be completely straight or close to it, when the pedals are at their lowest point, and your hips should not be rocking from side to side. Adjust saddle height as needed. Your saddle height is now roughly correct. It is possible your legs are different lengths; this process should detect that.

Second is saddle position fore and aft. There is individual preference involved, but the old rule - that your knee should be over the pedal spindle when the crank is pointing forward - is a starting point.

Third is cadence. Ride at 80 to 100 rpm.

Fourth is - well, you're not using clipless pedals, so we don't need to deal with cleat position or float. Just put the ball of your foot on the pedal. As you pedal, your knee should move up and down in a vertical line (viewed from the front of the bike). You don't want to be knock kneed or bow legged, if you can help it.

Fifth is not over doing it. Don't jump on the bike and pedal a lot further or harder or faster that you are used to doing. Take it gradually.

Let us know if your knees still hurt.