Backup User Files confusion

[mss]

Maybe it's just me, but the instructions on use of the "backup user files" using smart update seems misleading. I had a SuperDuper generated bootable clone of my main hard drive on a second drive. I've set a schedule for this to backup every couple of weeks. I decided to set up a second backup of just my user files to that same drive, thinking I was just going to replace just changed user files...NOT erase my entire backup drive with just my user directories.

Did I set something up wrong or is this the expected behavior. I was used to doing this with Synchronize Pro. I'd rather not backup the entire drive all the time in order to have a system backup that I can go back to if a major OS update goes bad. But I do want to routinely back up my user directory.

Thanks!