It is all about hearing engine's rpm's and timing.
Slowing down to a stop, with possible re-acceleration before completing stop:
1) Close throttle (and simultaneously brake if faster deceleration is desired)
2) At about 6K rpm, clutch-in and briefly bleep the throttle.
3) Shift down once while engine rpm's sound high (timing is key here).
4) Clutch-out (and crack the throttle open if synchronization was not perfect and you are dragging rear tire much).
5) Repeat the process to continue the slow down of the bike.
6) If the light suddenly turns to green, just open the throttle and hear what the engine is asking you to do.
7) Up or downshift as needed to put the engine in the 7K~9K rpm's range (between max torque and max power).
Unless your bike has a slipper clutch, increasing the rpm's of the engine for each downshift removes unnecessary stress and wear from the clutch plates, gears, bearings and chain.
http://en.wikipedia.org/wiki/Slipper_clutch