If what you want to achieve is beyond what is provided by the basic configurations in the Website Configuration Tool, use Advanced website customization, where certain levels of programming skills are required.
See Advanced website customization for explanations of the basic approaches of doing advanced customization in CONTENTdm using CSS and JavaScript. See Customization cookbook for examples.
The advanced customization will show you how to use the Custom CSS, Custom Pages and Custom Scripts in this part of the Website Configuration Tool.