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Hello

For example :
imagine a ball with a yellow car paint on it ( with flakes ). I want to add more one layer on my material, let's say a checkerboard pattern. But I want to have only the black ones visible and not the whites ( or reverse ).
How can I do this?

Add a new Layer to your material composition and make sure it's at the top of stack. Under Layer Properties on the right, you will see Opacity Mask slot. Place the checkerboard there and go.
For more:
http://support.nextlimit.com/display/ma ... ing+Layers

Great, so quite same thing with photoshop, thank you for the link