You can configure the template files visually using the Data Comparer Wizard. Set all the necessary options in each step of the wizard and click the Tools | Save template button. All the options will be saved to the template file which can be used afterwards in the console application.
The trial version of the utility allows to compare and synchronize no more than 10 tables. As for the rest, the functionality of the trial version does not differ from the full one. You can test the features implemented in Data Comparer within the 30-day trial period for free.
Follow all steps of the wizard setting the necessary parameters and save the project template at the last step of the wizard. The template can be launched from the command line of the console version of the utility. To schedule the project, set the console version run with the template name as a parameter, using the standard Windows Task Scheduler.