Best to keep it simple.
First, get a key storage cabinet big enough to hold every single key. Hopefully it will be expandable in case you need to add capacity later.
Second, number every door. Get a floor plan of the building and assign each door a number, one through whatever. Door 1 will get key AA1, door 2 will get key AA2, etc., using the locksmith's classic numbering system. Label the keys and store them in the key cabinet with the floor plan on which you noted the door numbers.
Third, group furniture and other non-door keys with the room that houses the objects they fit. For example, you have the office that takes the AA1 key. It has a file cabinet in it. Assign the file cabinet key the number AA1F. If it has two file cabinets, AA1F1 and AA1F2. You get the idea.
If you have a facility with several floors, you might consider having a code indicating what floor the door is on. For example, doors on the first floor might be numbered "AA1, AA2", etc., doors on the second floor might be numbered "AB1, AB2", etc., and doors on the third floor might be numbered "AC1, AC2", etc.
When you are done you will be able to go into the cabinet and find the office key. Near the office key you will find a key for everything in that office that has a key: cash box, workstation, closet, whatever. If you get confused you can consult the floor plan and get un-confused.
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