You will want to account for 2 separate items (3 if you are uploading a large ensemble piece such as concert band or orchestra) for covers to display and print correctly:

1. Cover Page JPEG file to go in the "Web Thumbnail" field - this will be the web thumbnail that displays on the website so customers can see your cover art when browsing jwpepper.com.
2. A score PDF with a cover page included in the file if you want your cover page printed on your score
3. (For large ensembles only) A wrapper PDF that will be used to print on the jacket that will go around your instrumental parts.

When uploading new music to My Score, you will want to have a cover page included in your score if you would like the cover to also be printed on the booklet of your score.  The wrapper will be in its own PDF file as it is a separate jacket placed around the parts in a large ensemble set.  

You can read more about wrappers in our support article on the subject here - What is a wrapper?