The array that I store the sequence in is a 100x3 2D unsigned long array. This needs to be stored into non-volatile memory so the board can be turned off and it still remembers the sequence when turned back on. I don't see this sequence being rewritten over 1000 times at max so I'm not worried about exceeding the rewrite limits of either the flash or EEPROM. At 100x3 it will have to be cut down a bit to (75x3 maybe) to fit into the EEPROM but I don't think I'll have to cut it down to fit into the flash as the program itself shouldn't use more than about 8K.
For the EEPROM, I kinda understand Halley's templates here: http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1234477290/3#11
But for writing to flash I am having a harder time understanding how to implement the example here: Frequently Asked Questions as it seems that you have to know the contents of the array when setting up the global constants.
Any help would be appreciated.