zarafamigrationCmdLine.exe from the migration program folder. If run with --help it will show the available options. If a config.cfg file is available in the same directory or specified by the -f command line option the config file will be used. See the Chapter 5, Appendix A; Configuration options command line tool for a peek at config file format.
zarafamigrationtool.msi and follow the necessary steps. Then start the migration tool itself: Start > Programs > Zarafa Migration Tool.