OK, let's say you've just set a conditional move in one of your games. On the CM page there's a grey bar at the top. You're in 'quick mode'. Click 'deep mode'. Now play your expected opponent's move, followed by your conditional move. Now play your opponent's next move and click 'record conditional move' and make your move.
At least, this is how I use it, but you could set up any position in there and if/when it arises whatever move you record will be played.