Well, if nothing else, you can put whatever you need into a script and run that, this should work. Code::Blocks can be told to run a script file given on the commandline.
Or, you could write a custom "compiler setup" plugin that makes whatever modifications you want on the first run (if some configuration file is present that tells it what to do).
Or, you can install Code::Blocks and edit the config file with a custom-made program/script afterwards (config is in XML format). Obviously, if this blows off your right arm, it's your own fault
