when I think of this problem, I think of a static cube with the colors moving across it in known patterns.  So....

A Cube object contains 6 Side objects that remain fixed indexed 0-5.
Each side contains 9 position objects that remain fixed indexed 0-8.
Each position contains a color.

For simplicity, handle every action in quarter turn increments. There are 3 axis of rotation, each in 2 possible directions for a total of 6 possible actions on the cube. with this information, it becomes a fairly simple task to map out the 6 possible actions on the cube.

So the color green in side 6, position 3, may move to side 1 position 3, or side 2 position 7.  I haven't explored this enough to find any mathematical translations, but patterns will probably emerge that you can take advantage of in code.