I don't use that specific program, but in general, yes, an OS upgrade preserves your applications. You're only upgrading the OS, not the applications. Thus, some apps may not work with the new OS until they also are upgraded.
If your files are properly saved in your User Account, among other "safe" places, they will not be touched. The key is to do an "Archive and Install" which will save the old OS until you are sure it can be deleted. (Like after you've had those "ah ha!" moments about something the old System had that you miss.)