I don't think I'm allowed to mention a specific product here, but if you search Google for "order management" or "inventory management" you will find that there are programs designed for ecommerce companies that will help you manage your inventory along with the rest of your business.
What options are available is also dependant on how complex your needs are.
* Do you need to accept returns or exchanges? * Does inventory status need to be reflected on your site in real time? * Are all of your stock units complete or do you have subassemblies that need to be put together into final goods? * Do you need for your inventory management software to warn you when certain thresholds are passed? * Do you want your inventory management system to automatically generate purchase orders to vendors to restock? * Do you need your inventory management system closely tied into your accounting system?
The more "yes" answers you have, the more you can expect to spend...