The EEC is, among other things, a few EEPROM chips which hold the settings. These are overriden by the external EEPROM chips, it's settings will take precidence over the EEC. If you get tuning software and *really* know what you are doing, you can reflash the EEPROM chips in the EEC. I do stress the *really* part as you need to know exactly what you are doing or you can make your car run like crap.
There are a few people who will fly out to dyno sessions and tune your car, if you don't have an external chip, they will reflash your EEC. The cost is usually more than a chip, but is tuned specifically for your car instead of semi-generic.
EEPROM stands for "Electrical Erasable Programmable Read-Only Memory". By exposing it to an electrical charge, a "Flash" of electricity if you will, you erase the contents and then can re-write to them (usually in the same process.) The chips come unprogrammed from the factory, and Ford flashes them to put on the settings it wants while the car is on the line. EPROM uses UV light instead of electricity.
If you've ever worked on your computer, here are some EEPROMs that will give you an idea of how the process works.
BIOS chip, allows you to flash it for extra options, extra CPU support, etc.
Modem EEPROM, allows you to flash it for new standards (the U.S.Robotics X2 to V.90 flash being the most recent I can recall)
Video BIOS chip, allows you to change hardware instructions on the card (as opposed to software changes like resolution and such)
DVD ROM EEPROM (also on set-top boxes), This is where they region lock the drives and why you can change the region a few times, it reflashes the EEPROM.
