SetSiteSecurity will shown you which Acl's will be set by the tool. The form shows you a grid with all the folders, registry keys and Http Namespace for which rights will be set on your server. The column 'Object' contains the name of the folder, registry key or Http Namespace, the column 'Group' contains the NT user for which the rules will be set, the column 'Access' shows the access level that will be granted to the user on the given object and the column 'Recursive' indicates if the Acl applies only the given object or also to all child objects.
Before the Acl rules are applied, you have the possibility to uncheck rules that do not comply to your company's security policy. Note that Smartsite needs access to all listed objects in order to work properly so if you uncheck a rule, you must add an equivalent or wider Acl to your server. You can use the validation option in SetSiteSecurity to check if your Acl's have the proper effect.