The traditional way to deal with this would be to use the Skyline user interface to create a Skyline document which contains all of the modifications that you need.
Then, your command-line program would never actually create a new blank Skyline document but would instead open the existing document using the "--in" command-line argument and save it as a different name with the "--out" command-line argument.

I know that in recent versions we have added many more command-line arguments for scenarios such as defining modifications, but I do not see any arguments that would work for defining custom modifications. It might be that the only way to define custom modifications from the command-line would be to generate the XML in the .sky file yourself.
-- Nick