Having duplicate folders (Inbox, Drafts, Junk Email, etc.) in the folder pane will be confusing for users. Example:
I'm not aware of any other webmail apps that do this. I suggest not duplicating the folders below the line. Instead, just show the user-added ones.
Maybe you're trying to copy Outlook with its "Favorites" section? If so, label the top part as Favorites (like Outlook does) and give the user the ability to add/remove folders from that section.