Do Ihave to list a course if I had AP credit

I took AP Physics B in high school and get a 5 - the credit shows up on my university transcript as "Physics XXX". I thought I wanted to do engineering so I took 'advanced physics for engineers" which was calculus based and difficult so I got a C semester I in mechanics and a B in electro/mag (also this is problematic because my university Physics I for engineers was 3 credits even though there was a lab - note: its good I took AP because engineering phsyics doesn't cover in depth all general pre med phsyics concepts like waves, optics, thermo, etc.).

Do I have to list these bad grades even though I have AP Credit for phsyics? they're obviously on my transcript but will I need to input into AMCAS for science GPA purposes? I have an A-/A- in gen chem, A/A in Bio and D+/A (retook Orgo I) and B- in orgo II.

Also is it bad I took pre-reqs at three different schools? I took my chem at my undergard university, then bio at a community college while doing my masters degree because it was cheap and the schedule fit with my other classes and oragnic at another school because they had an evening scienec program while I worked.

Thanks!