Overpronated Feet / Flat Feet?

[JTJet]

Today I went to a foot doctor and discovered I have overpronated feet and am flat footed. At least that's what I think I have. Basically, more weight is put down on the inside of my feet instead of being evenly distributed. The doctor got a mold of my feet and are going to make a pad for me to put inside my shoes.

I've recently been having some pain under my knees when applying pressure on my legs. This only happens after some running. The doctor told me that because my feet are overpronated, my joins in my leg got messed up.

Is there a way to fix the pain under my knee? I have been icing it down, but the pain always comes back. Will the padding that the doctor prescribed me help? Will I have to buy overpronated shoes? I'm not very knowledgeable in this area, so all comments are welcome.