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Coordinates specified are relative to their parent element. That is, the co-ordinates for a div on a page are relative to the top left corner of the document. The 0,0 coordinaties for a div nested within a div are the top left corner of the parent layer.
The problem with pixel perfect designs is the heterogeneity of the resolutions used by your users. Designing something to appear 900px to the right of the left of the page will mean that a user, whose reolution is 800x600, will have to scroll horizontally to see it. This is very important to keep in mind when using pixel perfect designs.