If you input one FF#, it sticks to the entire itinerary...and USUALLY, you cannot change FF# after you've flown the first leg of the itinerary.

I'd suggest NOT putting in any FF# and retro-claiming it individually after you've flown all of the flights. Or, are you ST E+ trying to get the elite benefits? If that's the case, I am not sure you'll get any since it's an EK codeshare (although I may very well be wrong)!