Hi, the only way I know to make the Magellan play with the white pieces from the bottom is to make the first move yourself and then swap sides so that the Magellan ends up making moves for White at the bottom. If you want the Magellan to pick the first move, then start a new game with Magellan playing white and record it's move. Then, start a new game with Magellan playing black and make the move it played for white. You will then have to take back it's reply as black, but can then swap sides and carry on the game with Magellan playing white from the bottom.

It's not ideal but does work. If you are pitting machine against machine, it's better to just rotate the pieces of the other machine - assuming this supports the option of course!