Adding Downloads
You can upload single files via eShop → Downloads.
Individual downloadable products/files can then be added via the Download dropdown in the Product Entry: Product Option pane in each products Post or Page.
Uploading Multiple Files
You can upload multiple files to wp-content\eshop_downloads using FTP. Then navigate to eShop → Downloads and use the Add all unknown download files link to add all of your uploaded files to eShop.

FlipFlop 3.0