They'll average every post-secondary level science class (biology, chemistry, physics, and math) into one BCPM cumulative GPA. If that entire GPA is really low, then it's going to hurt you when schools automatically screen out a certain threshold. You're not doomed completely by any means, but some schools won't offer you a secondary (but some schools give everyone a secondary, so you might be okay with those). However, if your cumulative is something like a 3.4+ and your current grades are a 3.8+ then I'd say you're in great shape.
Basically, they want to see if you're capable of a med school curriculum. If you have a positive upward trend (bad grades a long time ago are MUCH less important than good grades last semester), and good grades now, then your overall prognosis SHOULD be pretty bright. 🙂