Your trying to combine two seperate things into one. You tell Rhino cam where you want the part to be located in your part box or cylinder. You tell it where you want the stock box to be located by assigning the xz points, it then tells Mach where the part and the stock are to be located in relationship to each other. You set up a jig to hold your stock and zero your z, x, y axis, run your cuts. then repeat.
CHoose your stock profile .. box stock. part box stock etc (yellow box under the set up tab)
pick "set to box stock" option in the locate world coordinate system tab
Choose from the zero face buttons then the zero position buttons this will tell R/C where to Tell Mach you want to locate your work at.
Under the RHinocam 2.0 tab at the top of the page choose "getting Started" on the evaluation page that pops up choose "GSG"