Head to https://amtra5keyboards.com.au/firmware-builder . Either select your keyboard preset or upload a previous configuration.
Click on the Keymap tab and then on each key to assign your preferred layout.
Optionally, you may save your changes by downloading a configuration from the Settings tab.
Compile your firmware as a .hex in the Compile tab.
Download XLoader from http://russemotto.com/xloader/ . Unzip in to a directory.
Add this line to xloader/devices.txt.
Open XLoader and select your .hex. Select Leonardo(32U4).
Plug in your Pro Micro.
Short the GND and RST pins together twice in quick succession. Two red LEDs should come on. You now have 8 seconds to begin the flash.
Select the new COM port that has now shown up in XLoader.
If the upload has failed, try again from step 6.