You may want to consider sending a lower quantity to eBay and using inkFrog's sync settings to automatically restock eBay as needed.
Allow Separate Inventory Quantity for eBay
To enable separate inventory, select settings > store connector and then click the settings (gear) button on the right side of the page. If you have inventory sync on for Shopify to inkFrog, there is an option below that to allow separate inventory which when enabled, provides 2 quantity fields within your listings, one for Shopify and one for eBay. The eBay quantity may be at or below your Shopify inventory quantity.
The restock settings are based upon store quantity revisions. This setting will increase eBay's available quantity based upon restocking quantity on your store. This is useful when eBay and store quantity reaches 0, then the store is restocked, eBay will also be restocked based upon the value entered for this sync setting.
There is an auto restock option as well. When enabled, you're able to set a restock quantity. For example, if you set your eBay quantity to 1 for your listings, in the auto restock rule, you're able to set when quantity reaches 0 set back to a fixed amount of 1. So when an item sells on eBay, inkFrog would check your currently available store quantity and as long as there are 1 or more available, inkFrog would auto restock your eBay listing back to a quantity of 1. This setting is based upon eBay sales.
eBay Import Quantity Limit
There is also an eBay import quantity limit setting. If you set this to 1, when you import new products from your store, the eBay quantity will automatically be set to a quantity of 1 as long as your store inventory is 1 or above.