On a turbocharged engine, Upper deck and lower deck pressure in the intake system refers to what?

Maintaining 14.7 lbs per square inch though out the carburation system! Aircraft with normally aspirated engines lose power, which they are capable of as soon as they leave sea level altitude. The "blower" systems installed on internal combustion engines is designed to "fool" the aircraft engine in to thinking it is at sea level and depending on the kind of system and design, determines at which altitude the "blower" can continue to produce 14.7 lbs per square inch of atmospheric pressure to the carburation system. You can determine that maximum design altitude for "Blower" effectiveness by watching your manifold pressure gauge and when it starts to drop off, then you know that you have reached the maximum altitude of its assistances in maintaining a "sea level" pressure. It also permits you to fly at a much higher altitude than normally aspirated engines.
When I refer to sea level, I am assuming a standard atmospheric temperature of 59 degrees F. the changes in temperature as you climb will also effect the performance of the blower. Example, in a cold air mass, it would be more effective to a higher altitude than it would in a warm air mass, because of the density altitude!