I just made the transformation today from + to X. I have rotated my APM to face forward and it is my understanding that this is necessary. In terms of specifying the configuration, you can do this easily in the setup mode of the CLI from the APM planner or Arduino.
Hope this helps
Actually, this is what I see as well. As the APM is always pointing forward, no matter of the configuration, the compass also should point in the same direction. In my understanding, therefore the MP does not need to consider the configuration and the heading should be ok.
I was told by Chris that the heading of the compass might be off of few degrees due to some local influences on my board. As far as I understand, absolute orientation is not that important. It is important that the compass works correctly for relative rotations.