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We use the Advanced Assembly Extension (AAX) with top-down design to do this. You can drive sub-assemblies and individual parts from the top level assembly with this. Just FYI, we have 4 seats of Pro/E with only 2 of AAX. With AAX you can customize the program to be fully drivable, but you don't need AAX to actually drive the model.
Hope this helps,
Rodney (WF3 M140)