eUpgrade - Non-Elite & Elite + different booking ref, but same flights
You can make each individual request 96 hours priority to each individual flight departure. If you wanted to upgrade the entire itinerary, you would have to wait until 96 hours before the final flight departure.
Everyone here would recommend doing it for each flight as early as possible, unless you needed to consider strategic use of credits. For example, if you had an itinerary with short domestic + long international, you may want to hold off on requesting the short domestic until the long international is confirmed to avoid "wasting" credits on the short domestic if the long international doesn't go through.