You can set them in icconfig.xml and icrepconfig.xml prior to registration of the components using DU. DU(whether command line or GUI) will read the values from the icconfig and icrepconfig XML files and set them appropriately.
To modify the values in XML files, use Administrator GUI.
OR use IcStart on Unix or Server Manager on Windows.
Issue/Introduction
How to set non-default values to theworkflow server and Document repository server during Domain registration?