Have you tried? If you are referring to the section under settings>backup & reset>back up my data and automatic restore, it would surprise me if that type of backing up would cause any issues with ST. It's just backing up stuff like your wifi settings, searches you have added to Places/Maps and pictures associated with contacts. It's not like backing up a big file that is a mirror of your phone.
As far as a more substantial backup, you can use the new Carbon backup to back up a non rooted device, have the backup stored locally on the phone (on the virtual sd card), then, if the size of that backup takes up more space than you want taken, you can plug into your pc and cut/paste the backup files to your pc.