CR Notes and SO using secondary locations

I'm not sure where to turn with this one, but we're building new warehouses/business units here, where we will be using multiple items within a secondary location. This is the first time we have used this here, and are having trouble when creating credit notes, and will undoubtedly have trouble when trying to build a Sales order based on the items within this location. The way it is intended to work, is that a single item code can exist in more than one secondary location with in a specific warehouse. I'm under the impression here that primary locations are assigned a single item, and secondary locations may contain multiple items?

Is this something that is commonly done, or are we attepmting to create something that cannot be done? Anyone who as a setup that may resemble what I have described here, I would be interested to hear of any problems or alternative solutions that you may have used.

Cheers,
Jonesy.