Not matter if it's a Motel 6 or a Hyatt/Hilton/whatever hotel room, I give them a call 48 hours before check in, introduce myself, give them any room preferences, and just confirm that they know what time I'll be arriving.

Certainly helps if at Check In I don't have to request additional pillows [I prefer sleeping on something resembling a rock than a pillow...] or ask for soy milk or decaf coffee [both for my fiancee, not me], or ask for a non-smoking room.