What does it mean to 'run a store'? My boyfriends roommate is doing it and I have no idea what that means.

The inmate uses their commissary (and pay others for theirs) to inventory all of the popular items available and then sell to all the other inmates. The other inmates use the inmate's "store" to supplement their needs between commissary visits, or inmates that are on commissary restrictions.

The items you buy from the inmate store come at a premium - in most cases, you get one item and pay back with two of the same items.