I prefer togetherness
I am no expert (at anything much) but I remember flying Nomads, where it had been demonstrated tragically that the tail plane accumulated fatigue much faster if ground running assymetrically rather than both together. Perhaps this is limited to STOL aircraft with large tails or with rudders not held in place by a nosewheel connection. I generally find that airframe and rudder buffeting, not to mention noise and vibration etc feels more "comfortable" when you run up together or at least somewhat together, rather than individually. As for checking the flight manual, yes, but also consider checking service manuals for ground running procedures, of course not for pilot action but perhaps a better understanding of the issues may result.
Regards,