One of the way to tell PrestaBay what ebay category should be used for PrestaShop product it's set "Category" in Selling Profile. This work very good but only when you list all your items into a single category. Otherwise, you will need to create Selling Profile for every ebay category where you sell your item.
Another way to tell PrestaBay about ebay categories connection is creating ”Category Mapping”.
Every created “Category Mapping” can be selected in Selling Profile under option "eBay Category Mode".
List of Category Mappings you can find at page Catalog—>eBay—>Selling Profiles—>Category Mapping.
Every Category Mapping is created independently from ebay account and depend only on Marketplace data.