Unless you want to add 2 files for each product, I'll suggest you zip up all the files for a product together and upload them as a single file.
If you have a web developer, he should be able to use E-junkie for shopping cart and order processing and then use our integration and redirection features to build a download system on your end. That way, you can simply create only as many product as you actually have and since the download will handled by the download system on your end, it can server the right file using the style information we pass through. However, this will be complicated to build and only an experienced web developer can build this.