You can have your own Model01_Firmware.ino, which is the main file for the “sketch” (the Arduino parlance for the firmware project). This file is where all your customizations will be, while “updating the firmware” will probably mean updating all the Kaleidoscope libraries that your Model01_Firmware.ino uses.
Hopefully that makes some kind of sense…this thread may be of some use to you. Basically, you’ll have the Arduino-Boards repository, which contains all the Kaleidoscope firmware libraries that you can periodically update and your own Model01_Firmware.ino, which is the file that you’ll compile & upload to your keyboard (and which will #include the various libraries you need, pulling them from the Arduino-Boards repository).