I think this is the best way to handle this (I am SE and my wife E as well)

IF R available at T-7days, upgrade E on SE nomination
THEN, use E nomination for SE at T-4 with SE having good priority right up to gate time.

HOWEVER, if R space is tight, and there is a risk of only one upgrade coming available, it is better to use SE eupgrade for SE and waitlist E on their own account.

Permutation on this: If you have tons of eupgrade credits, you could use SE eupgrade account for both SE and E at T-7 and later on use the E upgrade account on flights that are wide open for both the SE and E.

I go through this agony every time we fly together TPAC.