To setup a manufacturing assembly, you should first create the 3 default datums planes and the main coordinate system you want to use. Next assemble the model that you want to machine to, (ref model). Next assemble the stock material, (workpiece). After that is done, pick "mfg setup" and create your "operation".
Once inside the operation, you will define the cell type,( lathe, mill,etc.), pick the coordinate system that you want to use, setup ant PPRINT comments that you want PROMAN to output to tape, and setup any fixturing that you want to use.
Once the operation is setup, you are now ready to create the NC sequences that you want to use, (holemaking, volume milling, trajectory, surface milling, etc.)
It seems like a lot to do, but you can save workcells, PPRINT setup, and even a generic manufacturing file to make it a lot faster to get going.