Pretty much any book by Silman is a wonderful reference that can answer these questions for you. I'll try to give a short answer, while highly recommending those books... You are referring to creating imbalances and then devising strategies that take advantage of them. Often times you may want to create an imbalance because (a) it's part of an opening that strives to create imbalances, or (b) the current board position calls for it. Recognizing this situation can lead to long term, or short term gains. One way to do this is as you suggested. It IS logical to eliminate your opponent's strength on such squares by, for instance, capturing their dark squared bishop. By doing so, they have one less attacker/defender on these squares. It then can become a leverage point that can guide down the road tactical play as the game progresses.
Key squares are similar, but aren't restricted to certain colors or squares. They depend on the current board situation -- What pieces are left, where they are located, and the pawn structure are significant in finding these squares.
I watch a lot of game analysis and lectures, and people are always talking about controlling squares. I understand that this means you have more pieces/pawns attacking a square, and usually that an enemy pawn can not attack it, but how is this turned into an advantage? What is the objective? To put a piece on that square?
And what about when they say something like,"White wants to trade off the dark squared bishops andplay on the dark squares" I would think you'd want your dark square bishop to play on the dark squares... Does this mean you have pawns that control dark squares and your oponent doesn't so you want to put your pieces there? But doesn't the opponent have the same option on the light squares?
And I'll often see them talk about getting an outpost for a knight as if it's checkmate. "Ooh, now white has this outpost for his knight and it can never be kicked out....What can black do here?"