To start with, you probably do not want to get multiple setups in Assembly Machining when using a common stock. Most of the time you just need the first setup with a perimeter feature to break the parts away from the common stock then you follow the rest through by using part machining techniques. If you really want to do assembly machining you will want to break away from common stock after the first setup. Think about using configurations inside CAMWorks or SolidWorks to make your work flow easier.
If you really need to do multiple setups in the same CAMWorks configuration think about how CAMWorks does Assembly Machining. The Assembly Level Setup, which drives the Operation Plan, will only produce if the spindle can see the face with the features on it (Example Below).
Now, if you need the second setup you will have to flip the parts in SolidWorks so the Spindle can see the face (example below).