I could swear that a Jet Blue phone rep told me it was possible to book a mixed itinerary when I wanted the online booking points for an underlying all-coach ticket that had been upgraded by phone to Mint for the first segment. He said they would give me the online points this time, but that in future I needed to book as City Pairs, or some such, myself. I just tried that and could only do coach for both segments, no way to mix them.