I think it would be smart and beneficial to put down all your science classes that are part of your BCPM GPA for AMCAS. I mean if you put down a few extra classes, whats the big deal. Its not like it was too time consuming.
I would definitely call the admissions office before submitting your secondary and get a direct answer from them. I didn't have a problem last year with the secondary, but it might be somewhat different this year. Anyways here is the number, (513) 558-7314