Apple announced during their iPad 3 event that the new iPad will indeed come packed with the rumored dual-core A5X SoC (system-on-a-chip) to power the device. It appears the quad-core aspect of the chip chip will be directly tied into the graphics subsystem powering the device.
There was some debate prior to the announcement that Apple might be using this dual-core option with the A5X instead of jumping to an A6 chip, but many believed that would cause slowdown with heavy multi-tasking, as well as hinder gaming performance as Apple pushes iOS further into the portable gaming realm. It was also thought that Apple would be utilizing both the A5X alongside the A6, but that's no longer the case.
The dual-core A5X with quad-core graphics should be enough power until Apple sees fit to introduce the more powerful A6 chip, which may also come in quad-core form but have a higher clock speed.