Mobile Site: Primary Menu

Hi, I'm still in the process of setting up my website. The mobile version of my website (http://goo.gl/49Mbeo) shows all the pages in the primary menu when the desktop version has these pages nested. I'm planning on having more than a few dozen pages, so it would be great to have the pages nested in categories like Finance or Department Store. Any help would be much appreciated. Also, if I switch to the Pro version, will any custom code I added to the Free version be different for the Pro version? Thanks!