The COmanage documentation has instructions and example CSS on modifying the default theme:

https://spaces.at.internet2.edu/display/COmanage/Theming+COmanage+Registry

A Collaborative Organisation (CO) admin can add custom themes within their CO configuration and a Platform admin can add custom themes to available to all COs. 

The COmanage platform supports loading images and other resources via URLs or they can be hosted by the service.