The short answer is that there is no way to combine PNRs, so given that you've already purchased these tickets, you're stuck on separate reservations. Thus, there is no way to list jointly for UDUs. You can:

1. Try to upgrade your wife with miles (she would need to clear before the 1K window to have much of a shot on most flights) and then hope you clear UDU. This is probably your best chance for both getting in F.

2. Give your wife your F seat if you clear (this is a popular solution in my household) and sit in her Y seat.

3. Offer your F seat to the person who gets your Y seat if you clear and you would rather sit together in coach. If you put your wife in the middle, then you could offer to the window person, and if they refuse, the aisle person.

4. Call reservations to cancel your automatic upgrade request. The possible advantage here is that once you're upgraded, your wife has no claim on E+. In some (uncommon) circumstances like a sweep or equipment subs, she may get reassigned.