A little more background would be helpful. You restored your entire backup? Why? I would think there would be an option to restore a particular file, and that you can choose to overwrite that file. I've never used TM, but another backup program (Retrospect) and that surely is standard.
So you know where all the restored files were placed, correct? If so, you can find the file(s) you wanted and move or copy it/them to your Desktop and then delete the rest of the restored files. Then place the ones you pulled out of there where they should go. Does that work for you?
Time machine should replace the files and not make another copy right?![]()
Again, I don't know for sure about Time Machine. (I don't know why others are not responding.) But, I think I'd want the file to remain and not be overwritten. Since you don't see the content of the file(s) you're restoring, how do you know you will like it better than what you have already?