It not seems as thing we can make fast and post instruction. There is lot of work mostly in layout as i understand. You'd better to submit ticket with request for a layout customization if you want it to be done by our side.
Or maybe do you want something specific from the screens, if so please clarify we will try to help.
You have to take coeds from home_header.tpl to your new design. Because flynax is based on smarty and it works on .tpl files. It will be difficult to add the script to normal php codes.
You can try to import your Auto Brand template to your new template.