E-Commerce Configuration Guide : Site configuration : Dynamic Master pages
 
Dynamic Master pages
 
For customizations, we can add custom master pages by copying MasterPage.master and modifying it. To configure to use the custom page, we change the MasterPage key to use a different master page. If mobile pages are being used, (EnableMobileMasterPage = 1) then the site expects to find a YourCustomPageMobile.master to use when in mobile mode.