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You will get miles for the flights and almost always for the hotel. If the hotel is some special discounted rate it may not give miles, but I have never had that problem.

If you don't need the hotel, there are times booking through the vacation sites is way less money for the same flights as the regular website, you just skip the hotel.

Just check the fare class of the flight to make sure, but unless they get really cheap and make changes you will get the miles.