Up and Down,
Yup, Juro's on it as usual. I think that either up or down should depend on the pattern and the conditions you'll fish in. Almost all heavy flies are tied point up. It's just a natural way to tie them. If the eyes are too big and you tie them on the same side as the point, they'll get in the way of the gap, preventing the fish from hooking itself.
Other patterns - like those for skinny water and stealthy presentations - can benefit from having small bead chain eyes tied on the underside of the hook. They just provide a little extra weight to get the fly down and ensure it rides hook-point down. This helps hide the shine of the hook and is good for spooky fish.
The only downside with the point down fly is that it is harder to hook bonefish with this type of pattern, especially if the fish tails on the fly. For bones, point up seems the best way to go.