Here are miscellaneous information for theming Mobile Joomla! sites.
Hiding mobile and web switching links
The mobile switcher allows the user to choose between web version and mobile version manually. Since Mobile Joomla! does this automatically based on the user agent detection you might want to hide this for aesthetics reasons on the web site. Note that if you disable it on mobile site also the mobile users cannot fallback to the normal web version.
Go to Extensions -> Module Manager. Search for Select Mark up. Disable one which is in footer2 (web site footer).
Mobile Joomla! templates can be overridden the same way as all Joomla! templates.