The Administration > Permissions section does not contain form that will allow you to set permissions over all modules. Currently the permissions are set through each module, since Administration > Permissions is used for setting global permissions.
You have to create a custom form where you set permissions for a given role and module.
ISecuredModule module = ModuleManager.WebModules[moduleName]
// here we set the permissions to our role called CustomUsers
ISecured permissions = module.SecurityRoot;
Here is our Permissions TOC that explains step by step and in details how to create custom permissions for not GenericConent based module
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