Fading "complex" object trough alpha [newbie question]

Hi all,
I’m a total newbie to blender. Currently using Blender 2.63 on a Windows-machine and here’s my problem:
I’m trying to create a animation for a presentation I have to create for university. The topic is about Rubik’s cube solving and I thought using some animations would make the whole topic easier to understand.

So I created a Rubik’ Cube model by using this tutorial-video: http://www.youtube.com/watch?v=4fs01zdvtg0 .

Now I would like to point out special cubies (a cubie is one of the 27 small cubes) by making the “uninteresting” cubies transparent. Each of the cubies consists of a simple box and up to 4 materials (the gray solid cube + up to three coloured faces).
But all e.g. “blue”-coloured faces use/refer to the same material.

I’m now trying to make a whole cubie transparent. But all How-To’s and post I’ve found just state, how to make a material transparent. but that’s not what I need, because when I make the “blue”-material transparent all blue faces are getting transparent and not only the one face of the selected box. On the other hand, the other faces of the selected box and the box itself remain solid.

Is there a “simple” way to select one of the boxes/cubies and to fade it to 50% transparency and back to solid state again or is it unavoidable to create separate materials for all faces and boxes?

As mentions before: I’m a total beginner and would be very thankful for broad explanations.

Thanks in advanced,

You’re going to have to make the material you want to change separate from the others. Best way to do this is to select the cubie who’s material you want to change, go into the materials tab and next to the materials name there should be a number, representing the amount of objects that reference this material. Click on it and you will then be able to edit its transparency without affecting the others.