You can absolutely use iControl to configure archiving of configurations. Here's what you should do.
1. Use System::ConfigSync::save_configuration() to create the ucs file.
2. Use System::ConfigSync::download_configuration() to download the created ucs file to disk.
In fact, the SDK has a sample perl script that does all of this for you. Check out the sdk_root/sdk/samples/soap/perl/soaplite/System/ConfigSync.pl sample and you should be all set!
In fact, this app also covers uploading and installing ucs files that you've previously backed up...
Good luck and let us know if anything else comes up...
-Joe
Nimbostratus