Time Machine takes care of itself. Time Machine is a mirror of your internal drive, with "snapshots" saved over time. When the Time Machine disk is full, the oldest "snapshot" is removed.
Time Machine has no notion of duplicate files -- it only mirrors what you have on your internal drive, so if there's duplicate files on your internal drive, Time Machine contains those duplicate files as well. If you delete a file from your internal drive, Time Machine will mirror this during the next Time Machine backup -- but you can retrieve that file if you need to by going "back in time" to a "snapshot" that occurred before the most recent backup.
Time Machine should never need any kind of manual intervention -- just leave it alone and let it do its thing. If you ever find the need to restore a file you accidentally deleted, or you find yourself needing to reformat your internal drive then restore all your data, then Time Machine will come in very handy.
If you cleanse your internal drive of duplicate files, then Time Machine will mirror this automatically.