I think it's mainly practice. Most puzzles can be done only in the top row if the clues are filled in there first, skipping clues that only pertain to the lower rows. Eventually, even the lower-row clues have limited possibilities in the top, and the answers become more obvious. Also, rather than writing things down, it seems to work to fill in what you can, as you can. Order is not important, as the clues and answers have a way of working themselves out as you go on.