Although we may make changes to the users, permissions part of the application, we aren't quite sure the changes you are requesting are in the current scope of FUEL. The permissions system is meant be pretty granular allowing you to create permissions and assign users to those permissions (as opposed to groups). That said, I could see there perhaps being a user group module and some changes to the user module that could be used to help assign users to groups instead.
The logic behind the permission is left up to the programmer how they want to implement it. For basic modules, there is a permission property you can set. The value can be a simple string or an array. If it is a string, it should match the name of the module (e.g. module_name='projects' should have a permission key of 'projects'). If the value assigned to the permission is an array, you can further specify whether someone can edit, publish or delete like the pages module (you can see it specified in the fuel/modules/fue/config/fuel_modules.php file). The fuel/modules/fuel/controllers/module.php file takes care of checking the permissions with the the Fuel_auth "has_permission()" method. Let me know if that answers your questions.
Comments
https://github.com/imknight/FUEL-CMS-Modules