It's only to stupid to take these before applying if you won't do decently. Someone will tell you you should get an A+ and you'll be okay, and while that's great advice, it's really hard to follow that advice. As long as it's as good as or better than your current grades for other courses, I'd say go ahead and take them. Just don't bomb the classes, essentially, and I'd say you should be fine (that's the advice I've been following myself...)
For Physics, each university breaks it up differently. I had a Physics 3 (not a sem school), which I loved, and despised my Physics 2, but I completed that before applying.
Currently, I'm taking Biochemistry, and even though I'm on SDN as a procrastination method (I have a Biochem final on Monday), I am actually enjoying this class. And please believe me, I do not enjoy these classes, but it's A LITTLE fun, because it's just memorizing pathways.
Look up at your school which course/prof is considered to be easier and take it from there, but I think it's completely okay for you to take one or the other or both after you have submitted your application, and put it down for Fall Semester's Planned Courses. Then later, you can do the academic update for grades, and the schools who really wanted to see one course or the other's grades will be able to interview you after that (I'm hoping that's the case for a lot of schools I've applied to--that they haven't invited me yet because of the outstanding requirement in Biochem, and they want to see how I fare in this course).
I wish you the best of luck!
