When layering clothes and boots it is actually very simple!!

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Make sure that the Item you want to have on top is above the other item in the dressing room. 

If you want boots over pants, make sure you slide them above the pants in the dressing room window. 

Same with putting a shirt over a dress.  Make sure you slide the shirt above the dress in the dressing room window.

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 I have found that sometimes after you leave it does not work.  Just go back and try it a second time and it usually works.