You don't have to have an E-junkie Shop that lists products in the general E-junkie Marketplace; that's a purely optional feature that would take extra steps to even set up.
However, the download fulfillment part of our service is designed for selling a regular product line, such as software, ebooks or music, where every buyer gets an identical copy of whatever file was uploaded for the product. We really aren't geared for providing a unique file to each buyer, nor do we have any way for buyers to upload a file for you to work on.
In fact, you wouldn't really need any special "download service" like E-junkie just to return completed project files to your clients. You could simply upload the file(s) to your own Web site or a file-serving service like Filevo, MegaUpload, Mediafire, etc., then just email the buyer with the URL to download just their own file(s) once you receive their payment. To request payment, you might consider using our free Buckdrop.com service.