C doesn't really have a multi-dimensional array. What is has is an array of arrays. You can write the data in the array to EEPROM in row-major order or column-major order, whichever is easiest for you to visualize. Just make sure that you read the data in the same order.
If I write these predefined values to EEPROM at the setup loop it will reset the updates at each restart.
But, you would only write them if there were new values coming from the serial port.