Backing a new account

i use a western digital Drive and super duper software to make the transfers.I set it up so that I have two partitions- one for all my files which acts like a clone and into which i intend making regular "smart backups", the other contains my User Files and also archived material which i have removed from my computer hard disk in order to make room (these particular files are all video ones).
I am little confused because Super duper *user notes* tell me that files are not bootable from here as its does not contain any operating system files and yet I can play my videos from there.Anyway be that as it may i am now wondering how i should set up Super duper for any further back ups into User files without losing any data that doesnt happen to be on my computer disk? Or would it be better to just click and drag from All files back up? I refer , of course, to files i may wish to archive in future.
Finally i set up another account for my wife and the same two partitions appear there.Now i am wondering what exactly happens ?Obviously there are no files in her account.If I did a back up from there would it affect my files and vice versa?Or would they back up independently of each other?Thank you

Get carbon copy cloner to make an exact copy of your old HD to the New one...
http://www.bombich.com/software/ccc.html
Have a look at Synchronize! Pro X 6.0.5
http://www.macupdate.com/info.php/id/6897/synchronize!-pro-x
Or the most expensive one & my favorite, Tri-Backup...
http://www.tri-edre.com/english/tribackup.html

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