I put all my biomede classes as engineering even if they were very prominently BCPM (biology, chemistry, physics, and math). The only biomede class I listed as a bio was cross listed in a bunch of other departments. This is for the AMCAS so it only affected my AMCAS science GPA, I was still able to use them for secondary prereqs if necessary. I don't know what AMCAS does when they verify transcripts, but I'd imagine that if there was a problem like listing a class they don't believe as a science or not listing sciences as sciences they would fix that, I mean it does take them a while to go through your primary.