I asked the same question in a different forum and got a very good answer.
There is a video link explaining it for a different camera, see below.
http://www.youtube.com/watch?v=KPdy52mR6Io
1. In general, the two IS systems are not compatible and make it worse when both are turned on.
2. The in-lens system is better so turn off the in-camera one. (Multiple reviews on dpreview.com confirm that as well).
3. You can always experiment and find out for yourself if you have such a system and post your findings for the rest of us to learn.
4. Manufacturers should figure out a way to design them to compliment each other, not "fight" each other for improved image stabilization.
Good luck.