Setting Folder Level Permissions
To set Folder level permissions, login into the web interface and navigate to the folder and select it.
In the security tab, select the "Manage Security" button.
Set the permissions allowed or disallowed for each user or group in this dialog:
It is possible to check the effective permissions for a user (not considering Share Permissions) by using the Check Access tab to check the permissions.
Effective Permissions only calculates permissions based on Folder Level Permissions and doesn't consider Share Permissions.