All that I know is that your deck can be on either side and so can your discard pile I believe. They just have to be on the opposite side of your prizes. Also I think that the discard has to be next to your deck but I'm not sure on that one.
Here is what the compendium sez:
Q. I like to keep my deck and discard pile sideways to help me keep them separate from my bench. Is that OK?
A. Your deck must be oriented vertically, to avoid revealing information during handling or cuts. You may turn your discard pile 'sideways', to help you distinguish it from your bench. (Oct 16, 2008 PUI Rules Team)
Q. Can I separate my discard pile in two stacks to make it easier to count energy?
A. No, you have to have a single neatly stacked discard pile. You may sort or turn cards neatly in that pile if it helps the game go more quickly, but they must all be touching. (Oct 16, 2008 PUI Rules Team)
The first is about the deck orientation and the discard orientation.
The second is specifically about the discard.
Hope it helped a little.