Sometime pedals are set up so your foot is at a slightly uncomfortable angle, and over a long ride that can cause knee discomfort. However if you adjust the cleats to the right angle, and if your cleats and pedals allow some "float" (at little looseness so you can adjust the tilt of your foot) you should be okay. Also try to use the lowest gear and highest pedalling cadence you are comfortable with ("spinning"). That is better for your knees than pedalling hard in a high gear ("mashing"). There's also a claim that shorter cranks are better for your knees, since you can still have the same leg extension at the bottom, but don't have to bring your knees as high at the top.