Using your hand, try to take the bathtub stopper out. Some models can be removed simply by pulling hard enough on them. However, if your bathtub stopper is screwed into the fixture itself, you are going to need to remove it with wrenches.
Take one of your wrenches and align it so it is under the lid of the stopper. You can then tighten the wrench so it grasps the bolt. This helps to ensure that the wrench doesn't move around while you work on removing the stopper.
Keep the first wrench where it is. With your second wrench, unscrew the cap that can be found at the top of the stopper. This should expose a bolt that fixes the stopper to the bathtub. Using the same wrench, unscrew this bolt. Once this bolt is undone, you should be able to remove the bathtub stopper and the first wrench from the bathtub by hand.