Before I figured all this out, I was shocked once to see extra e500's in my account after upgrading BOS-ORD and then ORD-YYZ with e500s.

I couldn't figure out where the extra e500s came from till I realized that I was charged for BOS-YYZ route only, even though the ticket was booked multi-city, and I actually stopped in ORD for most of the day...