Not using the "out-of-stock" listing feature on your Good Til Cancelled listings will cause overselling on eBay no matter what inventory management platform you use.
Any good-til-cancelled listing will stay active until explicitly cancelled and without the ability to mark it out-of-stock, we can never set it to 0 inventory. Instead, you will see errors like:
"The quantity must be a valid number greater than 0" or "Try enabling out of stock / good til cancelled listings"
To avoid this problem, ensure all of your Good Til Cancelled listings use the "out-of-stock" feature. This option is labeled "Listings stay active when you're out of stock" and the option should be enabled if you want to avoid overselling.
"Using the out-of-stock option on your Good ’Til Canceled listings may help protect you from receiving a transaction defect for running out of stock. [...] When the quantity of the listing becomes 0 (either because all the items were sold, or you adjusted the quantity), your listing stays active but hidden from search results." - eBay
If you are unable to use this option, it is not recommended but you may configure SKULabs to automatically close your listings when they are out of stock requiring you re-list them when the time comes. This can only be enabled across the board under credential settings. This alternative is not recommended and is only useful for a very small number of eBay sellers who are not yet using the highly recommended Good Til Cancelled / Allow out of stock configuration.