If you just had the "mandatory update" then you have FTM2012. It's mandatory as there are a number of fixes involved with it.
The "auto back up" feature has NOT changed. It hasn't changed for many years as long as you have it activated in the Tools, Options menu.
There is NO reason to work on an automatic back up file, unless you have a problem with your normal working file.
The help menu is VERY helpful. Don't know why you could not find anything about the option when you did the Help search.
Not sure what you mean by "doing my work from this AutoBackup while in Ancestry.com". You either work on your file from your PC with the Family Tree Maker program OR work on your Ancestry.com Ancestry Member Tree from your iPad.