Must I have my Deck above my Discard Pile on the field, or can I have it the other way around?
The Deck and Discard Pile must be on the same side of the field (either left or right), arranged one above the other. The standard play layout is to have the Discard Pile below the deck, but having the Deck below the Discard Pile is also permitted.
Source: TPCi Rules Team (2015-09-10)
Must I have my Deck and Discard Pile on the right side of the field, or can I have it on the left side (it's easier for me on the left because I am left-handed)?
The standard play layout is to have the Deck & Discard Pile on the right side and prizes on the left side, but having them the other way around is also permitted.
Source: TPCi Rules Team (2015-09-10)
Can I separate my discard pile in two stacks to make it easier to count energy?
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.
Source: PUI Rules Team (2008-10-16)
During a game is it legal to count your Discard pile? Is it also legal to count your deck as long as you do not look at the cards front?
Sure, though if you do it too often during a timed tournament it could be deemed stalling.
Source: WotC Chat (2000-08-31)
Some players freely examine their own discard pile (or their opponent's) whenever they want. Is this allowed? Or can a discard pile only be examined when you have official business there (like after playing Item Finder).
Discard piles are open knowledge (either player could look through them).
Source: WotC Chat (2000-04-06)