Have you looked in the acp > Look & Feel > Manage Skin Sets & Templates > Manage Templates for your skin? Click css and then ipb_styles.css . Now search for the logo and add what you want. Save it and refresh your browser shoing the skin.
You have to edit the User Agent Mapping settings for that skin and put the old IP.Board Mobile hidden for all groups and disable it.If you click "Manage User Agent Mapping" on the IP.Board Mobile skin you will see what things you need to check for the new mobile skin user agent settings.