1) Click on "Manage Inventory" under the 'Inventory' heading of the Control Panel.
2) Search for your item by it's Item ID (or Author / Title)
3) Scroll down to the 'Search Results' and click the 'Edit' link under your item.
4) Click on the 'eBay Properties' button.
5) Scroll down to the 'Stock' heading, here you can edit the quantity you send to eBay for your item. You can also limit the quantity a buyer can purchase.
6) When you are finished, be sure to click the 'Save Properties' button to finalize.