How to make transfer Time Machine back up to clean harddrive?

I have just recently upgraded to Mountain Lion but for some reason when it tried to restart, it wouldnt load past the first start up screen. Had to do a complete clean reinstall, and start from scratch. I just got done using migration assistant to copy what I thought would be everything that was backed up but only copied the applications and such. I still need all the stuff from my user file and the rest of everything. I plugged in the external back up and wouldn't copy. I read through a couple of forums and saw that I need to create a clone? Just curious on precisely what to do. When i look at the restore this is what comes up and I was not sure where to put the hard drive and the external drive in which spot. Also wanted to make sure I didnt mess anything up by just a lack of knowledge on my part.
I also noticed that I am not even able to copy anything to desktop or remove items from the quick startup bar at the bottom.
Thanks for taking the time to help!

peakaboo09 wrote:
I have just recently upgraded to Mountain Lion but for some reason when it tried to restart, it wouldnt load past the first start up screen. Had to do a complete clean reinstall, and start from scratch. I just got done using migration assistant to copy what I thought would be everything that was backed up but only copied the applications and such.
Did you use Setup Assistant when your Mac started up after reinstalling OSX, or did you set up a user account, then later on use the Migration Assistant app?  If you used Migration Assistant, your data is in the user account(s) you transferred, not the one you created.  See Problems after using Migration Assistant for details.

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