Welcome, Lovemybike!

On the knee issue:
you could always go back to your bike shop and get a refitting in a while, but I think Eden has pointed a very important fact: SPIN. Your legs should be spinning at a cadence of approx 85-95 RPM when moving along on flats. It will make a world of difference for your knees.

Otherwise, as a rule of thumb: pain in front of the knee, seat too low, pain in back of the knee, see too high. But it's really only a rule of thumb. If pain doesn't go away with spinning (or if you are spinning already), consider seeing a specialist instead of playing around your settings by yourself...

Enjoy!