The Advanced tab is mainly used for setting environment variables required for the appropriate RCS system. Not all RCS systems define or need these variables. Alternatively you can define the environments as part of your standard environment outside of CRiSP, but doing so from inside allows you to easily change the settings.
The various commands listed are used depending on the RCS menu command you select from the Tools menu. Each command is parameterized so you can easily tailor the command.