The Permanent Options window (accessed via the General Options button in the ribbon bar) enables you to specify settings that are to be used whenever you run SCS on this computer. These are settings that are not specific to any one production, but which are applicable or potentially applicable to all cue files used on this computer. The settings are save in the Windows Registry (current user) so are not transferred to another computer if you copy a cue file.
In the Options window there are seven groups of options, which can be selected by clicking the appropriate tab: