How do you train around a desk job that leaves your back and neck aching?

Two things independently: reduce the load and build capacity. Reducing load means breaking up sitting — a two minute stand every half hour does more than one long stretch session, and raising your screen to eye level fixes most neck complaints. Building capacity means strengthening what is weak, typically the upper back, glutes and deep core. Rows, face pulls, hip hinges and dead bugs cover most of it. Stretching alone tends to give short-lived relief because tightness is often a symptom of weakness rather than the cause.