First of all, all your templates and jobs will automatically be saved when closing the program (and automatically loaded when starting it again). You can find these files in the sub-directory “settings”of the program, the files are called templates.dat and jobs.dat. Please note that the job queue will also be saved each time a job finished its execution (so that you don't lose the progress of your jobs in case your computer crashes while processing).
You have the possibility to manually save and load other job queues (this might be handy if you are working on different projects). For this simply use the File menu and click on Load job queue or Save job queue respectively. The same applies to templates.