Could you provide more information on the problems you are experiencing. ?  As with all things on ebay I just keep it as simple as possible. All items listed show how many are left for sale. When I sell an item and the listing shows only 2 or 3 are left, I count up what is in storage at the same time as I find and pack the item sold. If there is a discrepancy, I ammend the listing there and then as I pack and have the listing on the screen.

If the listing is selling like hot cakes, I order more stock immediately, ( before I forget or get busy doing something else. ), I then just keep an eye on the listing to make sure it does not run out and lose my seller history. Sometimes I add the number of items on the order to the listing before I actually get them, to keep the listing going BUT I have secure supply arrangements that mean I NEVER have to wait more than 2 days for new stock. ( and have a 3 day handling period ) This last step could get messy if your suppliers and transport is not 100% reliable. There is a feature to keep a listing going, but show it is out of stock. I havnt used it myself, but others may be able to tell you how it works.