I'm not sure which extraction utility you are using for your .zip files, but I always select "Extract to Here" - this ensures that the folder hierarchy is kept, as Xrystal mentioned above.
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"You'd be surprised how many people violate this simple principle every day of their lives and try to fit square pegs into round holes, ignoring the clear reality that Things Are As They Are." -Benjamin Hoff, The Tao of Pooh
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