Don't know if you are still watching this but since you never got an answer:
Simple version:
If you are using the green key (1st key) and want to use the yellow key you stick the yellow key in and turn it. Some of the pins that allowed the green key to operate become "trapped" so they are no longer part of the pin stack. Now the yellow key works.
Use the red key for the first time after you have been using the yellow key and the pins to allow the yellow key to work become "trapped" and are no longer part of the pin stack.
It is like a construction keyed lock where the home owner can insert their key for the first time and turn it and little ball bearings that are the equivilant of master wafers get stuck in small holes in the cylinder plug so they are no longer part of the pin stack, and thus the builders key will no longer work. 3 in 1 is like that but with three keys instead of 2 and the innerworkings are slightly different.
Hopefully me over simplified example was helpful and also for more information read what zeke79 wrote in this thread:
viewtopic.php?t=12399