It seems to me like you want to create a custom theme, change the logo and edit the navigation menu to hide(?) the Manual button (if you want to change where it links to, then that can be done in CMS settings).
Regarding custom theme please see the following for more details - https://xibo.org.uk/docs/developer/custom-theme-development
Alternatively Xibo Signage also offers White Label CMS Themes if that would be of interest to you.