They can't run side-by-side at the same time, but you can swap between one and the other; just make sure you fully exit one copy first before swapping to the other copy.
(BTW, swapping between HDD and USB versions on the same machine will sometimes mess up the Windows 7 taskbar's jumplist entries for Opus, but they're easily repaired by making any change in Preferences which causes the jumplist to be re-generated. Unfortunately, it's a limitation of Windows. There is no way for a program to check its current jumplist entries, all they can do is erase the list and add new items to it (but not confirm that the current items are correct). Creating the jumplist is quite slow, so while Opus could re-create the jumplist each time it started, to ensure it was correct, that would slow down startup for something that is almost never needed.)