Recommended Products Templates
Copy the files from edd-recommended-products/templates/ to wp-content/themes/YOURTHEME/edd_templates/ and then modify as desired.
Single Item Recommendations:
To get the recommendations for a single page (single.php download post_type) use the supplied single_recommendations.php as a basic format to isolate the recommendations for this specific item. If desired, you can also supply the logged in user ID as a 2nd argument to edd_rp_get_suggestions() to remove items the current user already owns. In the default template this is not enabled, and users will see items they have purchased in the Single view.
Checkout Page Recommendations:
This page uses all items currently in the cart to build a recommendation profile. You can use the supplied checkout_recommendations.php as a basic template to get the recommendations profile, and if desired specify the currently logged in user ID as a 2nd argument to edd_rp_get_multi_suggestions() to remove items the current user already owns. In the default template this is enabled to prevent a user from buying items again, since they are 1 step away from final checkout.