I was under the assumption that Carmack's position within id was overseeing and directing the engine development. I think it's likely that he will retain that position but be more hands-off and give more weight to the boots on the ground's opinion on matters.
He spoke about his position at Armadillo Airspace during his Quakecon keynote briefly this year mentioning how he didn't feel comfortable commanding too much since he wasn't full-time like some of the other people working there.