if the sales man has any common sense he will sort it for you otherwise you need to look in to telling him you want you money back. there are laws and regulations that he must behold otherwise i wouldnt be very happy with him or the branch for selling a car that they didnt check thoroughly.
I had the same thing nearly a year ago and was lucky that they did any thing in the end but persevered and got it fixed under warranty.
its a common problem with these engines across the range (audis, seats, skoda's all suffering the same) so i suggest you say to them, not that you read something on the internet, but you are concerned that the car you bought isnt in working order and its nothing to do with the alternator they replaced but could be something else, like a friend said it was the cam belt and tensioner. if they dont sort it properly then they will be breaching the terms of the warranty.