Ethan, There are a lot of possible reasons why you could be experiencing knee pain and there isn't one cure all for all of them. Without more detail about your style of riding, your bike geometry, your cycling experience, how long you've had the pain, how it started, etc. answers would just be a guess.
"it's important to understand what makes them fast. It's more important to understand what keeps them from going faster." DS
Hello Ethan, I've been in your situation last year, especially after one very big workout which was too much for me. I was in pain for about 4 months. The reason for the knee pain could be very different from too low saddle to bad shoes. I would suggest going to your local bike shop with your bike and talk to the guys there. I'm sure that they will help you with this.