I've risked this a few times (on the Y/B labeled PIT-LAX/SFO fares). I place the CC information in, and then hit "apply upgrades." I choose to use 500 milers (since I'm CP and therefore have all I can eat). If you select the two (or more) flights to be upgraded, it will kick you into the "select premium seat" screen, where you can grab your F seat of choice. It will then ticket the whole thing with your original seat assignment in F.
However, because I've seen some weird stuff when using upgrades from "premium" award tickets, I still call the CP desk and verify seats that I've "upgraded at booking." Twice now, however, everything has worked just fine. I just bought number three today

.
------------------
Saving the world, one clue at a time.