This switch is located at Channel>Channel Settings>Ebay Settings tab.
You can select the category taxonomies from the dropdown box and apply them to the whole eBay channel. If you have more than one taxonomy, this is useful to determine which category taxonomy will be used for eBay. The selected taxonomy will be used for the eBay channel. This way you can create the products depending on the assigned taxonomy to the products. If you don’t want to use this feature, you leave it blank.
IMPORTANT NOTE: This setting will be applied to the taxonomy you choose, not all items in the channel.