Congratulations on making your mind so early about what career you want to pursue. Setting your goals early will definitely increase your chance to succeed in everything you put your mind to. Now, to answer your questions whether colleges look at physics and math grades separately, I would say it really depends on the college. They have different rules but do not get discourage by that. Math and Physics are challenging subjects and very few students apply to colleges with stellar scores. So I have few recommendations for you that should help you get into an engineering school:
1. Most important thing try to get high scores on the national tests (especially math)
2. If you apply to a school that specifically mentions the grades in high school as a criteria for admissions you could write a letter (1 page max) and explain why your Physics grades are not that great – a lot of schools want to see a candidate that does just good in school but gets involved with major related activities (e.g. engineering societies, projects – Formula 1 team, volunteering, etc) rather than have a 4.0 GPA and spend your time studying all day.
3. Last but not least you can always start at a community college and then transfer to a University. Not only the credit hour is cheaper (so you won’t rack up debt), but you can take Math and Physics classes and make sure you take a decent grade and then transfer to a University.
In conclusion – there are so many ways to get around the “not so great grades” that you took in high school; by all means do not get discouraged by that. If the University you want to apply won’t accept you, go to a community college for a year and then apply again as a transfer student (work with an advisor to ensure any classes you take at the community college will transfer to the University). Also, do not get disappointed by the possible Bs or Cs grades you may take while taking Engineering classes for the first time. Just hang in there and give it your all and eventually you will succeed. My grades weren’t great in my freshmen year, but by my senior year I managed to not only raise my GPA, but I also got admitted to a Master program that paid my tuition and a little money on a side. Remember, “It’s not over until it’s really over”. Wish you all the best!