Feng,
Again, I am sorry, but I don’t understand what you are asking when you say “sensitivities are applied to the upper layers”. Sensitivities are propagated through all of the model layers and all model processes. You can calculate the sensitivity of modeled species to emissions in the upper layer and/or you can calculate the sensitivity of species in the upper layers to emissions where ever you specify. So you can address any of your example questions by directing the model as is appropriate for each.
Sergey