The two emails from E-junkie would be (going by your numbers):
1. A product-specific thank-you email, which gets sent for each digital item and contains a link to the thank-you/download page for just that item.
3. Your Common Thank-you Email, which gets sent once for each order regardless of which item(s) were ordered and contains a link to reach the consolidated thank-you/download page for all items in the order (same page the buyer can usually proceed to after checkout).
For simplicity, we generally recommend disabling the product-specific emails; to do this, just edit each product's settings to Enable Templated Email but leave the Email Message field blank.
If you only have the one product, you may want to disable the Common email instead, as the product-based email allows more product-specific details to be inserted in your email template. To disable the Common email, just go to Seller Admin > Account Preferences and delete everything in the Common Thank-you Email field.
This help page explains more about customizing your thank-you emails: