The CKEditor.Java backend provides 2 ways to overwrite properties used by the JavaScript frontend (the editor).
Each property can be set by #setProperty of codes.thischwa.ckeditor.CKEditor, which will pass-thru to the frontend. Disadvantage: These properties have to be defined in every page.
Example:
CKEditor editor = new CKEditor(request, "field"); editor.setProperty("uiColor", "#AADC6E");
This should be the preferred way to set global properties and can be done by #setProperty, as well.
Example:
CKEditor editor = new CKEditor(request, "field"); editor.setProperty("customConfig", "PathToYourConfig.js");
It isn't required to use only one of the configuration options described above. Just keep the loading order in mind:
More details about the configuration settings can be found at Configuration Loading Order in the official developers guide of the CKEditor.