Update from the 31st of july, 2013. Crossed from Peru into Ecuador:
So the first big complex you'll encounter at the border (Peruvian side); ignore it as it's only for people entering Peru and drive on! You'll see another one, kind of the same, where you have to go to the Peruvian Immigrations and Customs, and then to the Ecuadorian Immigrations (all in the same complex). Afterwards, the Ecuadorian Customs are indeed where Laura says they are; some 3-5km further up on the Panamericana!
Try to be there before the big busses around midday, as immigrations is incredibly slow.
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