As long as you can get your HHonors number associated with your reservation BEFORE you arrive, you should be eligible for your Diamond possible upgrade. If you wait until you show up at the hotel to give your HHonors number, it may be tough to get an upgrade (rooms may already be pre-blocked and nothing better is available). Other than the upgrade, you should get all the Diamond amenities due you at the particular brand you stay at regardless of when you give them your HH number. And, yes, you may not get your points/stay credit with the 3rd party booking.