I don't see any problem with booking two rooms in the same city for the same time frame.
My last visit to San Francisco I booked the Hyatt Embarcadero and the Omni. If I didn't get upgraded at the Omni I planned to bail and go back to the Hyatt (closer to where I needed to be). I checked in mid-afternoon at the Omni, received my upgrade and promptly went online and canceled my Hyatt reservation.