smarty-plugins

I'm creating a store based on PrestaShop (v 1.6), and I want to register my custom modifier plugin to be accessible from any templates (includinf front and back-officetemplates). The question is where to place the registration code? Now I use a Tools class override to add function to handle modifier (that is acceptable practice in case of store-specific functionality, afaik), and smarty.config.inc.php to register plugin (because all PrestaShop plugins are registereg here), but this file contains a warning about "not to modify file directly" and, as far as I understand, will be overwritten when