All Magellan themes are stored in your Templates\Magellan Themes folder. Several different example theme folders are added on installation for different colors. You can choose one of these to update for your theme, or add a new folder.
The folder structure in your theme folder should match the default Magellan engine folder. So if you want to update a css file, your theme folder should have a \css sub-folder that contains the css file, or to use your company logo on the site your theme folder should have the \images sub-folder that contains the logo image file. You only need to add a sub-folder if you are customizing a file in that folder.