I do not see in Miniprog3 user manual any references to programming
EEPROM in addition to FLASH, or for that matter any output hex file
format that includes EEPROM data from the linker. The only api I see
that can put anything into EEPROM is Keil MON51, and appears to be
restricted to the debugger.
You could always consider a modified bootloader that could have the
additional capability of running EEPROM APIs.
The PSoC programmer user guide (version 3.15.1) says in part 2.12:
Because the PSoC 3 and PSoC 5 hex files do not describe EEPROM data; PSoC Programmer does not support EEPROM
programming from the GUI. PSoC Programmer allows you to clear EEPROM data after programming PSoC 3 and PSoC 5
So this leaves only the boot loader method dana mentioned.
PSoC 3 and PSoC 5 hex files do not describe EEPROM data. PSoC Programmer does not support EEPROM programming.
The PSoC Programmer COM does support EEPROM actions at the API level, which allows you to create scripts or utilities that perform EEPROM actions. These examples are detailed in the Examples folder in the root installation directory of PSoC Programmer:
In Creator 3.0 there is a new tab in the .cydwr view: E²Prom. There you may edit the eeprom contents for your need and program it together with the project.