Acne: Is it bad to apply Clinique (dermatologist tested) foundation to cover my acne during the day?

Does it cause any damage?
OR should I leave my acne alone, and wait until it goes away naturally?

To be honest, to put any kind of foundation over a pimple will risk it getting worse if not infected. Wash your face thoroughly with warm water and soap. When you rinse you face, rinse with COLD water, to close open pores. If you don't want to try that, I would suggest washing your face with lemon juice, it's acidity will destroy anything unclean on your face, including pimples. =)