If you create a custom template for an existing configuration file, even if there is no corresponding standard template fragment, it will be processed. For example, if you create a fragment "15mycode" in the templates-custom/etc/hosts directory, it will be processed along with the other fragments.
If you create templates, custom or otherwise, for config files that don't already exist as templates -- for example, for /etc/rsyncd.conf -- then you have to create the appropriate action script in /etc/e-smith/events/actions, and also link that action into the appropriate event directories.