GD Mail Queue plugin runs initialization and other things very early in the plugin loading process, and a lot of filters and actions are fired before the theme is even loaded. So, adding custom code to control GD Mail Queue into theme functions.php file will not work for all the filters and actions.
The best way to add the custom code that hooks into the GD Mail Queue is by using Must Use Plugins. WordPress supports Must Use Plugins or mu-plugins since version 3.0, and they are the best way to add custom code to WordPress for the purpose of tweaking. So, to add custom code for GD Mail Queue plugin, make sure that your website has a folder called ‘mu-plugins‘ in the ‘wp-content‘ folder. Once you have that folder, create a new PHP file in that folder. For example, make the empty file called ‘gd-mail-queue-tweaks.php’. When empty, this file needs only to have php opening tag:
<?php // add custom code here //
When you need to add some tweak related to GD Mail Queue plugin, add it into this file.