On this page, you can set up the automatic synchronization of Amazon FBA Product Quantity with your Magento Inventory Source.

FBA to Magento Stock Synchronization

Enable this option if you want M2E Pro to automatically update product stock in your Magento Inventory Source based on the quantity of the corresponding Amazon FBA product.

Source

Once the QTY value of an FBA product is reported by Amazon, it gets imported into the predefined Inventory Source. Select the needed Inventory Source or create a new one by clicking Manage Sources if you don't want the FBA product stock information to have any effect on your Magento inventory.