Has your regular season concluded? Once it does the "Playoff Setup" Menu in the Commissioner section should contain options to set up your playoffs pretty much any way you want. Consolation Brackets, 3rd Place Game, whatever.
"I disapprove of what you say, but I will defend to the death your right to say it." -- Voltaire
You should be able to set up multiple consolation brackets from the playoff setup option under the commish menu. You may have to wait until after the first playoff week to set up the bracket for the losers since I'm not sure the setup allows you to automatically assign the loser of a particular game to a particular consolation bracket. You will probably have to select the manual setup option.