You are making the transition from discussing "electronics" to discussing "semiconductors". The Wikipedia entry has a good introduction of how electrons can flow through this seemingly reverse-biased "collector-to-emitter diode":
A "model" for an NPN transistor is two diodes back-to-back, as you describe, but you cannot just put two diodes back-to-back and have yourself a transistor. You really need to understand how semiconductors work at the physical level, as described in the Wikipedia article above (briefly), and in texts on semiconductor theory. For example, electrons are actually going in the completely opposite direction from what you describe (emitter to base and collector), but from an "electronics" viewpoint we don't make the distinction (and it doesn't matter). But once you start discussing "semiconductors" then it matters.
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