Im no Steve or Rounik but as you havent had a reply to this I thought I would help if I can.
By Midi regions that are stacked im presuming you mean multi take recording - where after several passes the midi files are stacked above each other on one track? If you wish to add automation to these takes you first have to seperate the tracks. This is done by clicking the arrow at the top right of the top midi part (the top left arrown reveals all your takes for selection) and selecting one of the various options - seperate all to individual tracks,seperate selected to individual tracks e.t.c. Once seperated in the way you choose these tracks can then be edited, automated like normal mide tracks.
As for automation of mod wheel, pitch bend e.t.c this is not accessed in the normal automation way (as youve prob guessed)
Click on the midi region you want to automate, open the piano roll and click on the tab in the bottom left. You will see another window opens up under the piano roll grid. Click on the button in the bottom left of this new window to show a list of variable parameters that you can automate. Pitch wheel and modulation being one of the many.
Hope this helps...apologies to Steve H and Rounik for lowering the standard of help at MPV