I would try different shoes. If they're that uncomfortable, I don't think you should try to break them in. I think you risk injury. Running shoes should be comfortable or close to comfortable from first wearing. I have high arches, but I pronate (the two are often thought of as mutually exclusive, but they're not; they're just a bad combination). So I need high, stable arch support. My favorite shoes are Brooks Adrenaline. I don't even need insoles for the newest model. They're expensive, but they're less expensive than a joint injury.
ETA: Ah, I misread. I thought you were saying you needed high arch support. So scratch that about the Brooks shoes. But I still think you should go to a running store that analyzes your gait and looks at your feet, the way you put pressure on your feet, etc. You could save yourself a lot of grief.