As a general rule of thumb ...

Store program code in Flash. Flash is less expensive than EEPROM and usually denser. Generally, you update code infrequently (except during debugging) so the longer Flash erase/re-write time is negligible.

Store constants or persistent data in EEPROM. An EEPROM write cycle is simpler and faster. EEPROM is usually more expensive and smaller density.

Both are non-volatile memories with similar characteristics. Most modern versions of Flash and EEPROM have the programming circuitry on chip.