Commercial airplanes operate in auto mode when it comes to pressurization. After takeoff the cabin pressure altitude will slowly climb as the aircraft's altitude increases. The cabin pressure altitude will increase until it reaches approximately 8,000' and then it will hold steady as the airplane climbs. Pilots do have the ability to manually override auto mode. However, it's a bit of a tedious process to continually monitor and adjust the cabin altitude as the plane climbs and descends. Manual control of the cabin pressure is usually reserved for emergency/irregular operations.
As far as affecting the structural integrity of the airplane I'm not certain if it would negatively affect it that much. The airframe always expands and contracts as the pressure changes and over many flights (>20,000 flights) eventually the structurally integrity will be compromised. These are 25 year old airplanes already, however they won't see anything close to the typical airline workload with the Pats operating them. So any effect on going between auto and manual mode would probably have minimal impact on the structural integrity. I think the bigger problem is that most aircraft are programed to drop the oxygen masks when the cabin altitude exceeds ~14,000' so that would be an issue. I'm not certain what the FAA (regulations are a bitch) would have to say about operating an aircraft on manual mode all the time. My guess is that it would be highly frowned upon... not to mention that you could kill off the entire organization from oxygen deprivation if the pilots were careless.
edit... Ahh you we're pondering increasing the cabin pressure to a lower altitude... eh, I think the FAA wouldn't approve of those operations but I could be wrong. Also I'm not sure if the pressurization system would be strong enough to hold a differential pressure that great between inside and outside the aircraft. I just fly em, I don't design em. We need an aeronautical engineer!