But it really should not matter when storing the value to EEPROM, as long as you read back in the same order you store. Storing two bytes (or any number of contiguous bytes) would have a starting address and length, the actual data contents, and what that data represents in the code, should be irrelevant. The only time I can think it would matter is if you wanted to dump the contents of the EEPROM to a human-readable format, but if you reversed the endianness between EEPROM and memory a similar dump of memory would not match and make things even more confusing.