I'm thinking that you might be using Options currently, instead of Variants, as Variants support stock levels per variant.
Example using X-Cart Demo:
http://www.x-cart.com/demo/admin/home.php << Go here to login
http://www.x-cart.com/demo/provider/product_modify.php?productid=16123§ion=variant s << This is a product using Variants, note the "Quantity in stock" that handles inventory level per variant, independent of the overall Product's inventory level.