Leonardo -
Use the Data command to write your value to EEProm when the chip is initially programmed (use for a static value or to preload the EEprom).... OR.... you can use the Read & Write commands to read or write data during program execution "Runtime" (like if the variable changes). Look at Section 5.11 for the Data command, 5.64 for the Read command, and 5.86 for the Write command.