Cheat. Put you setup assembly in a new assembly. Copy the subassembly where you want it and copy your toolpaths.
After using HSMworks you may not like Camworks very much.
I tried HSMWorks and hated it, couldn't make the switch. I know or maybe should say knew quite a few HSMWorks users that have since moved to other software and said they didn't like what Autodesk was doing with it. I dont know any specifics but just know a few that have left HSMWorks.