How to Separate Multiple Sites

We are a large warehouse facility with several corporate stores of our own. I have begun implementing the Avaya system in one of the stores as a second site which has allowed me to create separate IVRs for the store. But the separation seems to end there. The phones at the store can call any extension at either location as well as the paging system at either location. It would be ideal to have multiple locations as separate locations and then allow access to select extensions and not give store employees (or disgruntle employees) the ability to directly call our CEO. While looking at this situation I also realized that if I call our main line, when the IVR answers, I can dial the paging extension and send a page to any paging system at either site... from my home phone. Please advise as to how these can be resolved.