Thanks very much 
I'll start having a read.
As another example: I have a megasquirt ecu, I can change the fuel table values using the tuning program (tuner studio) these table changes get sent to the ecu.
How do these changes get made to the ecu? The software interface can read and write values to the ecu and im not sure how any of this works. Perhaps the software interface which updates the microcontroller in the ecu has a specific name that I can google for? Flash editor etc.
Sorry for the very specific example, it was the only thing I could think of whilst writing.
Rob,