"So my columns are anodes driven by the 595's through discreet PNP transistors."
So you have 64 PNP transistors? And then 8 NPN transistors to enable the 8 layers? With 9 shift registers?
Sparkfun has a series of tutorials on using Eagle, I would start there.
In the end it comes down to having good component placement. Without that, routing becomes a nightmare with vias all over the place trying to have signals crossing over each other.