You can turn on inventory tracking for items when you go to the Catalog tab and edit an item. 

What this does is that every time you issue an invoice from billing, it automatically deducts from your inventory.

The reference number is used for OR tracking in case you receive new stocks for your item. You will have to enter this manually on your end. For incoming transaction, you usually put the OR number or the delivery receipt number when you receive the item. When deducting from the inventory through the billing module, that reference number is automatically set.

This also helps for your book keeping purposes in case you want to double check the history of your shipments. 

Also, when you track inventory and issue an invoice, the reference number for the items going OUT of your clinic will be the corresponding billing invoice so you can better track where all your items are going to.

Currently they all show up in the Inventory, but you can opt not to put stocks in them. 

When you add a new stocks, one of the required fields would be the clinic. You can just leave the rest of the items in those clinics without stocks.