The Premier League champions were undone in the first-leg by Antoine Griezmann's controversial penalty but are set to welcome back captain Wes Morgan after he recovered from a back injury that has kept him out of the last six games.
Morgan watched on in Madrid with Diego Simeone and the hosts keen to see Jamie Vardy booked - which would have forced him out of the second leg - while sports scientist Tom Joel was sent from the dugout after the Atletico bench complained when he tried to hand out water to Marc Albrighton.
And Shakespeare has warned his team not to fall for any gamesmanship from the La Liga side this time around.
"Our players have to be smart, we have to take our own house and get that in order, we can't worry about the opposition's bench - we'll let the officials take care of that,” he said.
"We have to be mindful in terms of us being smart and our game management has to be good. We have to be aware of all those things. Ultimately we have to get our own house in order.
"We will focus on ourselves but be aware of Atletico. We know what we have to do and we can't sit back for 90 minutes because we need to score.
"There are different ways and come the game we'll find out if we've found a solution."
Morgan is set to return after coming through training following his back injury, although Shakespeare will leave the call until the morning of the game.
"The final decision will be made tomorrow. I need to see if there is no reaction," he said. "He has trained the last three training sessions in which the intensity has been greater every one.
"I am pleased with how he has progressed. I would like to find out from the player how his thoughts are. But my eyes tell me this morning we both should be fairly pleased how he has come through."