Calvary8561,
It could be a pulsating vaccum that keeps the beads agitated, but more than likely you have some photodetectors that are looking at the different colors.
As for how to start, you must figure out what causes the action, or what your PLC Outputs will be. In other words, once the sensors detect a bead of a certain color, what action must be taken to separate it from the others? Do these "cylinders" that you mentioned push a bead out of the chamber once a certain color is detedted, or is there a solenoid-operated gate or valve of some type? As most students do, you are trying to start with the wrong end of the program, and as usual, are having trouble seeing the forest because you keep looking at those trees (bead sensors) and can't imagine what to do with them. Forget the sensors for now and think about WHAT causes the beads to be separated.
Once you figure out what causes the RESULTS, then put a rung in your program for that, even if you leave the left side blank. It will be a place to start and a way to "organize" your program. Add any other auxiliary Outputs needed (counter, timers, and so on). Then all you have to do is figure out what inputs, either external or internal to the PLC, are needed to control the outputs. Now when you get an idea of how the program will work, then you can write the pseudo-code very precisely.