Once the class library is finished compiling the interpreter looks for a file at
Platform.userConfigDir +/+ "startup.scd" and if such a file exists, executes any code within it (this happens within Main: -startup). By creating a file in this location you can make user specific customizations.
~/.config/SuperCollider/startup.scd, according to the xdg base directory specification
C:\\SuperCollider\\startup.scd(or similar, depending on the location of the SuperCollider installation)
A common example would be to alter the options of the local and internal Servers:
Naturally the file must contain only valid SC expressions.