That is what i do now for multiple day stays on a cancelable rate. Book each night separate. Complete flexibility. I can come later, leave earlier, add night before or after without loosing my rate.
Its not much more time consuming online, but the benefits outweigh the additional work. At check in i hand them a printout of all reservations and let the hotel deal with them. Never had a problem staying in the same room or needing to check out/in.