I don't quite follow what you mean about automatic vs. manual cart, so I'll offer some basic explanations that may answer your question.
Once you set up your products in E-junkie Seller Admin, we provide you with ready-made HTML codes for your cart buttons. You would simply copy the codes from us and paste them into the HTML source of your own Web site pages, wherever you want our buttons to appear among your own layout, text and images. Our standard cart would appear as an overlay "inside" your own page, fitting within your site's existing layout and branding, or you can use Buy Now buttons that bypass the cart to take buyers directly to instant checkout for just one item at a time.
If you are selling a file download, you would simply upload that file to our server when adding the download product in your E-junkie Seller Admin. After the buyer finishes checkout, and once the payment processor notifies us they have completed the buyer's payment, we grant the buyer access to a thank-you page we automatically generate for their transaction, where we would present their unique download link(s).
We also send the buyer a thank-you email message with a link to reach their thank-you/download page in case they did not proceed there after checkout. Every download link we issue expires after the number of Attempts or Hours (whichever comes first) that you specify in each product's settings.
If PayPal has notified you of a payment, but E-junkie did not seem to process that order, please follow the troubleshooting instructions on this help page to sort out that problem:
http://www.e-junkie.com/ej/trouble.paypal.order-not-processed.htm
