Go to the Application Data group, Files and Folders view in the InstallShield IDE.  In the Destination computer's folders pane, find the directory you want to set the permissions for, right-click it, select Properties, then click the Permissions button.  A dialog box will open where you can set a Domain, a User, and the permissions, including Full Control, Modify, Read & Execute, List Folder Contents, Read, Write, and Special Permissions.  Just set what you want and that's it.