Thank you all for your help!
Another question I have is if you did poorly in whatever science class but score amazing on that subject in the PCAT, does it show? And if it does, would it even be considered?
The answer is both yes and no.
The PCAT is graded on 5 "subjects"; Verbal, Quantitative, Bio, Chem, and Reading Comp. If you get a C in Orgo II, it won't show on the PCAT if you improve your knowledge of the subject per se, but a high score in general in Chemistry on the PCAT will demonstrate an obvious knowledge of the subject.
For example, if you know the material, but the instructor's exams just simply do not mesh with you (And this does legitimately occur in my opinion, occasionally [not to be used an excuse for overall, chronic poor performance of course]), you can show it on the PCAT.
Whether "it will be considered" is, to me, a confusing question. Are you asking if the PCAT-Chemistry score itself will be considered (in lieu of your passable, but not amazing, Orgo grade?), as if overriding past poor performance? It's possible. As long as your GPA gets past the "first cut", and with a high PCAT I'm sure it would, I doubt you've got anything to worry about.
I advise against re-taking a single "C" course unless you're absolutely, positively, 130% sure that doing so would result in an A (i.e., you KNOW your instructor simply creates exams that are confusing). Otherwise, a single C will not harm you overall (Folks in UCSF sometimes have Cs on their transcripts, it's not a deal-breaker).
As others have said, if you're a >3.0 student, then don't fret the C(s). Use your time to volunteer, get your CphT, or just practice to blast the PCAT. All of those would be, in my approximation, much more time-efficient for you than re-taking a course you got a C in, only to maybe repeat a C or even worse, get a D or an F.