The Supercube can be solved normally, however, at the end of the solve the centers will be twisted the wrong way, the following shows how to fix them.

Press Play on the first cube to half-twist the centers on the front & top faces. Press Play on the second cube to half-twist the centers on the front & back faces. The same sequences can also be used to quarter-twist the two centers (on moves 3 & 7) but they must be turned in opposite directions.

The following sequence from Twisty Puzzles half-twists the center on the top face only. The single half-twisted center can be avoided as shown here.

You can try solving centers on the Supercube here.