Please note that when preparing your stock items for Amazon, the way the system matches when uploading stock item levels is as follows:
If you have only one code against a stock item and it is the stock barcode, you can just define the stock code as the matching criteria.
If you have multiple codes against one stock item, you need to define a barcode, for example Amazon SKU, for each one. Therefore, in the stock item you will need to add the different codes for the item by adding the Amazon SKU barcode multiple times.