Stock tracking does not need to be activated globally for the store. Instead, you can apply just to the items that you need to track stock for.

When creating or editing a version, check the 'stock tracking' checkbox. There are two relevant text fields: the actual stock quantity, and the warn level.

When the stock quantity reaches the warn level or below, a stock warning will appear in the 'To Do' list on the right hand side of the back end. This way, you can re-order more stock before your supplies are exhausted.

Items which are out of stock will have their 'Add' button on the front end replaced by an 'out of stock' message to prevent the items being purchased.

You can use the frontend.orders.allowpurchaseoutofstock config setting to allow out of stock items to be purchased on your store.