there is only one EEPROM so you must use it the same way the firmware does... or you will break it for the rest of the firmware
EEPROM is for mostly storing data between reboots. (often configuration data)
It is limited to 100,000 writes and then it will just not work any more. (It literally wears out)
(if your wanting to store lots of changes, you will need to look at wear leaving algorithms etc, which is a huge topic in itself)
The EEPROM space is very limited 4096 bytes total.
There are 4 things to change
1) increment the version number
2) SettingsDataStruct , you add your data structures you want to save to this (is only used in calculating EEPROM size)
3) modify MarlinSettings::save to save your data
4) modify MarlinSettings::_load to load your data