Does the configuration of a confined layer change the storage? I have a confined aquifer of sand. I will temporarily drain the aquifer, remove the top one meter of the aquifer and then replace that with a layer of gravel. After that I will restore the layer (and the aquitard above it). After that, it is a confined layer again. 

Is the storage of the aquifer different with the small layer of gravel?
Under normal conditions a layer of gravel has more hydraulic conductivity in comparison to sand. Check this table with a hydraulic conductivity k per soiltype 

The storage in the aquifer with gravel will be larger than in sand if the same thickness is used. Otherwise you should take the thickness into account as well (= Transmissivity: kD).