I bet your fellow GTDers on these Forums will give you some great advice. As a staff person and coach I can tell you the difference:
Making It All Work is much more strategic and broad. It's described as:
If you already have a good grasp on the basic GTD workflow models, and/or are looking for inspiration from David and a broader understanding of the whole game, you will get value from this course.
Mastering Workflow is much more tactical and specific about implementation. It's described as:
If you are new to GTD, or have implemented the system but are looking for tactical implementation advice, you will find this seminar to be a good launch pad for getting your GTD system off the ground.
Hope this helps!