Hi ciggy,
It's a very interesting theory. The only aspect that seems problematic is the logistics of having Atlantis' fleet of warships and military personnel that far from and above the sea holding sway over large portions of the Mediterranean.
Plato's account places the city within 5.7 miles of the sea and allowed that merchant ships and triremes entered the city day and night. It is really hard to picture 1,200 large ships each said to maintain a 200-man crew being ported up and down the Andes, several each day.
-Doug
The waters of Lake Po'opo are saline, which technically could classify it as a "sea" by ancient standards, and South America was completely laid out with highways by the builders of Tiwanaku. The commerce by sea and canal would have been for transport within the metropolitan area, while the logistics on a wider scale would have been based on port cities throughout the periphery of South America, many of which are probably now undersea sites--but the highways are still there so one could theoretically follow those to get an idea of where to dig.
Update: the Incas were reported to have reused the highways for their own Empire so that gives us a pretty clear picture of the logistical network, for the most part:
