FHR is an eligible booking channel, so you will (or at least you should) receive the Amb 1-cat upgrade in exactly the same way as if you had made a paid booking through ihg.com. Ditto with the Citi Prestige 4th night free.

It seems to me that the best thing to do is send an e-mail to the hotel with a list of the different bookings, and discuss your requests and what they can provide.