If a business has more than one restaurant (Subways) and makes deposits for all of them under one tax ID # and to one account, what address is used for the CTR? Is a P.O. Box accepted in these situations?

We have a similar situation with Gas Stations, and list the location that the owner uses as his primary office location.
I would try to get a complete address and shy away from PO Boxes

Actually, the instructions on the CTR itself state that a PO Box can only be used if there is no street address. I would say that if there is a physical Subway or gas station, then you cannot use a PO Box.