If you have a product with variable options available in the store front that require individual inventory tracking go to the selected product.
Scroll down to Pricing / inventory and set the inventory to Track with options.
Once you saved this top the product, you will see the stock field change to edit.
On editing the inventory you are taken to the combinations page, there you can enter the quantity in stock for each variation.
Inventory will then track the sales of each variation until zero stock.