Strictly speaking, HHonors does not allow a single account to be used jointly.

However...just book it in her name on her account, and add your name as the 2nd guest (there's an option on the booking page to do this). When you check in, provide the reservation name and your card to pay for the room. If they ask where Mrs. Phoenix is, tell them she's running late.

I may get flamed by the sticklers here since she technically should be the one checking in and staying (with you as guest).