Originally Posted by SAN 1K

It is my recollection (though I could be corrected on this) is that if you call into reservations, you can request that your upgrade be applied to only one segment of a direct flight. So if there is one that you would rather have, you can try to clear on that first. If it clears, then you can subsequently request the second leg.
I believe this is a common technique for those who have "direct" flights that include a domestic and an international segment - and don't want to risk losing a confirmed upgrade cert for the domestic leg only.