Using the Migration assistant to restore a Time machine back up

[cap2587]

I am using the Migration assistant in my mac to restore files, folders from a time machine back up. I would have thought that all the information be put into the respective folders. However, it seems like it dumps it all in the one folder and you are expected to copy and past it into the new destination. My applications are the only things going into the right area. I am also getting a small red symbol in my folders and I cannot open them due to lacking the necessary permissions. Am I doing something wrong? Thanks for the help.