Thanks for your kind words. I am really glad that you like our solution :)
1. You don't need to create separate entries for items you are selling on eBay, unless the title of your listing on eBay does not match the product name you are using on your website.
If you do end up keep them separate for any reason, you still only have to upload file for one of them. For the other, please use "files from other products" option to use the file from the other products.
2. You can create coupons that work for all your products in E-junkie Seller Admin > Cart Discounts
3. Sure, E-junkie Seller Admin > View Summary.