You have the option of "Preferred coach ID" while booking a ticket via IRCTC. If you enter any coach number on the DD (ie C1, C2 etc) with the suffix U, you will get a seat in the upper deck of that coach subject to availability. There is absolutely no difference between the process followed by IRCTC and at a counter to request a specific coach - in either case the preferred coach ID will be conveyed to the PRS for allocation if possible.
Also, I have clarified with PRS officials and it is indeed true that the lower and upper decks of DD coaches are treated separately by the PRS. Charts are no longer pasted on coaches, but...
more... when they were, there were always separate charts pasted for seats 1-75 (lower deck and mezzanine) and 76-120 (upper) with different coach IDs (C1L and C1U). There was also a brief time period when indianrail.gov.in used to display the number of coaches of each class of a train, and for DD trains the number was always double of the actual because of this reason.
You are welcome to go to any knowledgeable reservation supervisor/charting staff and ask about this if you do not believe me.