Should I call or email the hotel? Should I just wait til I arrive and hope that they can accommodate me? Should I call Hilton Reservations and make sure that there's still a note on my reservation?
Contact the Hotel and politely ask!
Here's a situation I faced recently.
In April we wanted to book three nights at the Rome Cavalieri in September using my freshly earned Q3FN's.
With the Q3FN's one needs to telephone HHonors as you cannot book with these certificates online.
To check availability I looked at the dates for an award and only Twin was available for the first night. Both Twin & King options were available for the other two nights.
I called to make two separate bookings for 1 x Twin and 2 x King as we wanted king (not living in a 50's sitcom either), but the agent would not do this - only offering Twin for three nights with a note that our preference was for "King". Having other pressing issues at the time, I accepted this with the intention to revisit it later.
Shortly after the booking confirmation I received a welcome email from the hotel. Using the contact information on this replied about our situation and a request for 3 x King. I had a reply within a day confirming this and our booking promptly showed online as King for the three nights. 
Of course not all hotels have the availability to do this, so YMMV. (Of course, if you
do not ask, it makes it a lot harder to receive!
