For ease, I would book both rooms under one reservation. In the past when I have done this at Hilton properties, it seems to increase the likelihood of the points for both rooms to both be credited to my account (as they should be). Just make sure both rooms are on one folio and you pay for both with the same credit card.

If you need to cancel the second room later on, I can see where you might encounter difficulties by trying to do it online, but if you call the hotel directly to make the change, it shouldn't cause you any problems.

Calling the hotel directly to change the reservation usually seems to yield me the best results - both when adding a second room to the reservation at the same rate I got the first room AND/OR if I need to cancel the second room on my reservation and want to make sure I don't mess up the reservation for my room.