To add new templates, create a custom JavaScript file containing your template definitions. You can base your file on the built-in default.js file that can be found in the plugins/templates/templates directory of CKEditor.
When your definitions are ready, use the templates_files configuration setting to point to the custom template definition file.
config.templates_files = [ '/mytemplates.js' ];
More details on defining custom templates can be found in the Templates article of the CKEditor 3.x Developer's Guide.