A little more info that may be helpful...
The examples referenced by Jarrod contain a .NET constructor to create a System Definition file by giving a name, description, creator, version, etc... If you double-click the constructor node it will bring up a dialog which show all the constructors for the SystemDefintion object. You should see another constructor which only requires a "nivssdfFile" string input. Use this constructor instead and provide a path to your nivssdf file to open your existing SysDef (instead of creating a new one).
Remember, you still need to call the SaveSystemDefinitionFile method when you're done with your changes to commit everything to disk (as demonstrated in the example).
