Managing configurations via EEPROM by writing it with the hex file
AVRDUDE can program EEPROM. I usually do this as part of the firmware burn - the operator can pick which config block should go into the board while running the programming cycle. In some cases the EEPROM info is even generated programmatically during the cycle to contain dynamic info like unit serial number and commision date.

Here is an example command line that will program the file filename.hex into EEPROM...

avrdude -c stk500v2 -P COM6 -p atmega328p -U eeprom:w:filename.hex:i


The AVRDUDE write command (U) has many options to do almost anything you want...

-U memtype:op:filename[:format]
Perform a memory operation. Multiple ‘-U’ options can be specified in order to operate on multiple memories on the same command-line invocation. The memtype field specifies the memory type to operate on. Use the ‘-v’ option on the command line or the part command from terminal mode to display all the memory types supported by a particular device. Typically, a device’s memory configuration at least contains the memory types flash and eeprom. All memory types currently known are:
(...)
MEMTYPE:
eeprom
The EEPROM of the device.
(...)

OP:
w
read the specified file and write it to the specified device memory

(...)

FILENAME:
The filename field indicates the name of the file to read or write. The format field is optional and contains the format of the file to read or write. Possible values are:

i
Intel Hex

s
Motorola S-record

r
raw binary; little-endian byte order, in the case of the flash ROM data

e
ELF (Executable and Linkable Format), the final output file from the linker; currently only accepted as an input file

m
immediate mode; actual byte values specified on the command line, separated by commas or spaces in place of the filename field of the ‘-U’ option. This is useful for programming fuse bytes without having to create a single-byte file or enter terminal mode. If the number specified begins with 0x, it is treated as a hex value. If the number otherwise begins with a leading zero (0) it is treated as octal. Otherwise, the value is treated as decimal.

a
auto detect; valid for input only, and only if the input is not provided at stdin.

d
decimal; this and the following formats are only valid on output. They generate one line of output for the respective memory section, forming a comma-separated list of the values. This can be particularly useful for subsequent processing, like for fuse bit settings.

h
hexadecimal; each value will get the string 0x prepended.

o
octal; each value will get a 0 prepended unless it is less than 8 in which case it gets no prefix.

b
binary; each value will get the string 0b prepended.

The default is to use auto detection for input files, and raw binary format for output files.

Note that if filename contains a colon, the format field is no longer optional since the filename part following the colon would otherwise be misinterpreted as format.

As an abbreviation, the form -U filename is equivalent to specifying -U flash:w:filename:a. This will only work if filename does not have a colon in it.


Any of these files types can be used depending on what kind of data you are writing to the EEPROM and how it is being generated. 

More info here...
https://www.pololu.com/docs/0J67/5.8