This involves a whole bunch of steps. Here's what I did, and hopefully one of the least painful ways to do it. I used Windows 7.
Summary:
Step 1 - Decide on layout/layers, save as .json.
Use http://www.keyboard-layout-editor.com/ to generate a .json file with your layout/layers. Select "Default 60%" layout to get started.
Look for the .json export and save it out. You can also copy/paste it from the "Raw data" tab. You'll get a file that looks vaguely like:
["~\n`","!\n1","@\n2","#\n3","$\n4","%\n5","^\n6","&\n7","*\n8","(\n9",")\n0","_\n-","+\n=",{w:2},"Backspace"],
[{w:1.5},"Tab","Q","W","E","R","T","Y","U","I","O","P","{\n[","}\n]",{w:1.5},"|\n\\"],
[{w:1.75},"Caps Lock","A","S","D","F","G","H","J","K","L",":\n;","\"\n'",{w:2.25},"Enter"],
[{w:2.25},"Shift","Z","X","C","V","B","N","M","<\n,",">\n.","?\n/",{w:2.75},"Shift"],
[{w:1.25},"Ctrl",{w:1.25},"Win",{w:1.25},"Alt",{a:7,w:6.25},"",{a:4,w:1.25},"Alt",{w:1.25},"Win",{w:1.25},"Menu",{w:1.25},"Ctrl"]
for each layer
Step 2 - Build the firmware online (TMK)
Go to http://kb.sized.io - this lets you build the firmware online. Hit "upload .json" and upload the json from stage one.
Go through each stage, making sure each part is correct. Use this mapping ("AVR") column to help you do the mappings.
Make sure each column has a pin, and each row has a pin. No room for any LEDs.
Diode Direction - Column To Row
Bootloader Size - 4096KB
If you press "Download configuration", it will save a .json file with all your pinouts and all the work you've done on this site. You can
use this again on later if you need to rebuild the firmware (e.g. change key layout, or you messed up the pins).
After you're all happy, press "Download .hex file". The .hex file is the compiled code that goes on the pro micro. It is already
compiled for you on via the website. Pretty neat!
Step 3 - Getting the .hex file onto the pro micro
This part involves lots of steps. Here is my experience, though you will probably want to read other peoples guides and form your own idea of what to do.
First, a brief explanation on bootloader mode.
The pro micro has two modes: "regular" mode and "bootloader" mode. When in regular mode, it runs whatever code was in the .hex file.
When in bootloader mode, it sits around, letting you flash a new .hex file. To Set your pro micro to bootloader mode, you have to:
Step 3.1 - Making your computer recognize the pro micro
Step 3.2 - Flashing the firmware
We use a program called "AVRDude" to push the .hex file from our computer to the pro micro
avrdude -p atmega32u4 -P COM4 -c avr109 -U flash:w:filename.hex