Is there a way to distinguish the U1/U2 from stickminer, so I can put in different clock commands for each?
To the base cgminer it appears as a U3 at this time, so the frequency setting should already only apply to the Compac.
I recommend grabbing the custom cgminer build that actually recognizes the stick as a Compac, though. See first post for more information. Alternatively, try using bfgminer.