if your ponds are above ground, you can build a water way with window. see this pond to get some idea
http://photobucket.com/albums/y63/Koi38/?start=40 it looks pretty cool, imo.
if you ponds are both in-ground ponds, what's the purpose of having the underground swimway when you can only see top view? unless you plan to build underground view room. it's over killed for koi, imo.
if you really want to spend serious money, check out what they have at the rainforest cafe restaurants. two hugh cylinder tanks on both side of the restaurant entrance connected by huge overhead clear waterway for viewing fish swim between the two tanks.