Are you talking about the folders in the Bookmarks Sidebar, on the left-hand side of of the Safari window? (Most of us tech geeks would consider the "Bookmarks menu" to be the Bookmarks drop-down menu at the top of the screen.) I'll assume you're talking about the Sidebar for now...
You were editing the Sidebar (clicking the Edit button at the bottom of the sidebar), and you managed to delete the Bookmarks folder from within the sidebar? That folder normally can't be deleted or moved. If so, some damage may have been done "under the hood." I leave it to someone else to suggest a fix (probably involves trashing a plist file).
Or did the sidebar itself disappear? If so, go to the View menu at the top of the screen, and select Show Sidebar.