I pre-ordered skyrim on skype and i still paid $59.00 everywhere ive seen it's $59.00 but amazon sells it for $49.00 how can they do that?

They can sell it for however much they want. If they feel they can still mark it down and make a profit, they will. That's out of the developer's control at that point

Retailers don't pay what consumers pay for games. That's how they make a profit.