When I deal with Multisite installation.Some themes like mystique and aparatus provide the widget areas with in the theme-settings page to enter Advertising codes in the form of HTML or java script .But I want the 'Ad code Boxes' to access only by super admin(Me on my Multisite) and not by Normal admins .Can I make that boxes available only to me?
If that is custom functionality in theme options page then it is highly specific to that theme. Likely you will need to edit theme files and/or create child theme. Plus option pages can be simply in WordPress API but just as well can be built with help of theme framework or other kind of third party code.
I think your first stop should be developers of themes and information on how to best work with their option pages.
Take a look at the Capabilities plugin - Capability Manager (Wordpress Plugin) . You can give finer grained access to existing or new roles than you can with the default roles.