If your menu does not function correctly (e.g. disappears behind your media, ad region, or it is just difficult to hover and click with a mouse), then you probably don't have all of the required CSS for the menu in your Theme's CSS file. We recommend that you look at the code in the activated Theme at the sandbox site, which you can access at the link below.
Search the contents of this file for "software_menu", and copy and paste all of the CSS elements into your site's CSS Theme file. Then tune these CSS rules until you get the menu placement and styling you desire.