You can put system commands in a DITA2Go macro. A macro consists of a special configuration-file section to which you give a unique name; you invoke the macro by assigning its name, enclosed in <$ >, to a System*Command keyword. See §37.1 Defining and invoking macros.
For example, suppose your workflow requires backing up your DITA files to two servers. You could define a macro to supply the two copy commands, and assign that macro to a system command:
[Automation]
SystemStartCommand = <$backup>
[backup]
copy <$$_currpath>\\*.dita x:\\backup
copy <$$_currpath>\\*.dita "y:\\my other\\backup"
Notice the doubled backslashes (required in DITA2Go macros, where backslash is used as an escape character), and the quotes around the path that includes a space. See §37.1.1 Defining macros.
Comment out commands in macros
To omit running a particular system command without actually deleting the macro line that executes the command, you can “comment out” the command by preceding it with a semicolon. For example, suppose you do not always want to create a second backup:
[backup]
copy <$$_currpath>\\*.dita x:\\backup
; copy <$$_currpath>\\*.dita "y:\\my other\\backup"