Write code in here.
There is no relation with Custom Theme and Footers.
Manager wants to obsolete the Custom Theme Features so, try to solve your problem with others features.
Search the forum, footers and other new features will not work with any custom theme, only the inbuilt theme will use them. We are currently in an in-between phase where customization works but does not allow the use of new features such as footers and where the new system to help with more customization of the look and feel is not yet developed. So you either continue until the new system is in place with your custom theme(s) and not use any newer feature such as footers or use the inbuilt themes but forgo customizations such as colour in tables.
To put it simple. If you wont to use all new bells and whistles of Manager, say goodbye to theming in the moment. You are stuck with default theme and that is that.