I'm a newbie too, and I totally agree with getting the bike properly fitted. My friend is a physiotherapist, and a mad keen cyclist, and he helped me a lot with setting up the bike. I had both knees in pain, and what it was that I was reaching over too far and putting too much pressure on my hands, and not sitting on the bike properly.

So we adjusted, the cleat positioning on my shoes, the seat forward quite a bit, seat angle up a bit, and seat height was lowered half an inch. And bingo The bike is now AWESOME!!

Don't put up with the pain, it shouldn't have to hurt.

Take care out there!