The package generated with xSQL Builder also provides command line arguments that allow you to overwrite some of its settings. You can still run the package with no command line options and it will perform exactly what you had specified when you configured it. With the command line options you can overwrite settings such as the destination database or the custom scripts, so that you can use the same executable to synchronize multiple client databases without rebuilding it over and over again.
You can inspect all the command line options in the code template classes that shipped with xSQL Builder. You can add additional options as well. The Appendix C lists all the supported command line options.