Hi Mike, our system will not automatically remove any of your inventory options, so you would need to log in and manually disable an option in the event that you sell the last remaining piece of a particular item. You could then add the option back in when the item is back in stock.
Inventory management at the level you're describing may be available in a future version of the Online Store. I'll be happy to pass your feedback along through the proper channels for review. Thank you.