Hmm...I'm not completely sure how it would work for Orbitz/Expedia/Travelocity. I feel like I've had friends book on one of those engines before, and I was just able to call EXP and have them move their seats for me. My complication is usually corporate travel agents.

AA used to let my corporate TA request preferred seats electronically, but probably due to past abuse, it's now a manual process. I have to call my TA, give them my traveling companions' info along with the seats I want assigned (based on what I see on EF), then TA calls EXP, and finally EXP assigns the seats and pushes the seat info back to the TA. Tedious - yes, but do-able.