Can my program store sensor values to the on-board EEPROM (ie. datalogging)?
No, on-board EEPROM is reserved for your program and any constant data (eg. text messages, conversion factors, etc.). After programming, you switch the WRITE PROT switch on, preventing EEPROM from being written to. To log data values, (eg. sensor values), you should store them in serial EEPROM or serial Flash that you interface to the SPI port.