If you setted up the theme in the default config., just go to System > Manage Stores > click the Store View (for example French) and change the Code field to the identifier of the theme you are using with the name of the language you setted up. For example, if you are using hellokids, then the code will be hellokids_french.
Using the default config, will keep the language switcher in the header.
Hi, of course the template is adopted for multi-language usage, you have to modify the place of the language switcher in your styles.css, try this:
styles.css line 554:
float: right; padding-right: 55px;ADD THIS padding-top: 82px;ADD THIS
If you want to use flags, you will have to find the images and adapt them to the size of your choice. Check this example of a client: http://waimeabrands.com/