confused

I was diagnosed with pcos and the gyno wants me on birth control asap. she also gave me medicine for a yeast infection, she said its ok to take them both the same day so I did. its been 2 days since taking the yeast infection pill and I have to take the last one tomorrow, well there's still a smell, no itching or burning and I'm starting to spot. she said spotting Will be normal since its my first time on birth control. my question is will the yeast infection medication still work since I'm spotting?