At my school for the kids who are a year ahead in math senior year, we can take AP calc BC or another class called SUPA calc. SUPA calc is an equivalent to AP calc AB. I can only take the SUPA one as of now. Will this reflect badly on my math skills when applying?
I would say do not worry. I know plenty of people who applied engineering and were accepted having only taken AP Calculus AB. As long as the rest of your transcript reflects passion for your major you should be fine.