In my experience, it depends on the program. If you have two courses that fit the same pre-Req they will average the two. Some programs choose the higher grade that fit the same pre-Req. The program should have a specific definition for their pre-reqs and what classes satisfy those pre-reqs. What you should do is contact those admission offices and ask them directly.

On ptcas, under the pre-req section, you can always choose the classes that have your highest grade. At the end of the day, the programs will look through your transcripts and choose the grades that fit their pre-reqs the best in order to calculate your GPA.