We don't really list your files together in any sort of files-and-folders motif; instead, each product would have a single file uploaded to it. Did you actually mean you wanted to split your products into separate groups somehow?
You could open a separate E-junkie account for each group of products. Just bear in mind that products from different E-junkie accounts cannot be added to a buyer's cart together, so you'd want to be selling each group of products on separate sites. You could also just use Buy Now buttons (instead of Cart buttons) if products from different accounts are being sold on the same site together; however, Buy Nows have some limitations:
http://www.e-junkie.com/ej/help.buttons.buy-now.htm
