You are supposed to take your aligners out to brush your teeth, you simply need to rinse them and place them in a case while you brush and floss. Be sure to brush your teeth every time that you eat so that you are not trapping food particles or bacteria in between your teeth and your aligners. You should also floss at least once per day.
When you wear clear aligners, you can smile without it being obvious that you are undergoing an orthodontic treatment. What will be obvious is that your smile is looking better. Since the aligners are clear, you can see the position of your teeth. This is a huge benefit because as your teeth become straighter, your appearance will improve, rather than you waiting until the very end to benefit from the changes.