FHR absolutely allows you to enter your loyalty number in the booking. There is a field for it if you book online. Or the agents can do it for you if you call. However sometimes you need to call the hotel chain to ask them to put it in manually if it doesn't show up in your upcoming bookings. I and many other Flyertalkers have done this for years with IHG, Starwood, etc. You can fully stack the benefits, and often get a better upgrade than normal.