In the Cup summary page, click on the button, 'Insert Round'
Then name the round, something like '3rd place playoff',
Then set the Insert Round option to be 'After' 'Semi-Final'
You will now have a new round in the cup, now you have to Override the Round Entrants.
Click on the Entrants tab, select the newly created round for 3rd place from the dropdown, the click on the blue button, 'Override Round Entrants'
In this Round Entrants page select the dropdown, Create Round Entrant: 'Stage: Knockout, Round: Semi-Final - Loser' - press create.
This will make it so that the losers of the Semi-Final round will go into your new round.
Then the last step is to amend the Round Entrants for the Final, so from the Entrants page, select the Final, then click on 'Override Round Entrants' button, then select the Create Round Entrant to be 'Stage: Knockout, Round: Semi-Final - Winner' then press create.
All the rounds will be setup correctly and you will just need to assign the entrants for the new 3rd place round and create the match.