In the CBFM directions it says that if you get AF in the night, set the monitor to CD1 the following morning, and that if you get AF during the day, to set the monitor to CD 1 the next morning.
Myself as well as a bunch of other ladies on here just set CD 1 to the day that AF shows whether it's early that morning or sometime later during the day just so that the monitor days match up to your charting days if you temp (or if you don't temp, so it matches your cycle day count in general). If AF comes during the day after the time that you would set for your testing window, you can just set it for CD 2 the next morning during when you want your testing window to be. (Testing window is three hours before and three hours after you press the M button to start out a cycle.) If you want to set it to CD 2 (or up to CD 5), just hold down the M button until it reads the day that you want.
Hope that helps!