Standing up and being a bit looser and more relaxed on the pedals and bars will generally allow the bike to move a bit more freely over the roughness and presumably take a bit less impact, but in the end it probably makes no real difference as long as you have a well built bike/wheels. 'Riding lightly' can save you a good bit of discomfort over rough patches because you allow your arms and legs to absorb shock as opposed to staying sitting so all the shock is transferred directly to your ass.