Butler (Tool)
Use the tool provided by itch called 'butler'. Check it out here
It is easy to use and lets you avoid any manual file upload to itch directly.

I use the following 4 commands to publish my game
- butler push webgl user/game:webgl
- butler push windows user/game:windows
- butler push osx user/game:osx
- butler push linux user/game:linux
Steps for building
- Create a Builds folder in you game folder (MyGame/Builds)
- Create folders in Builds for each of your build targets (webgl, windows, osx, linux)
- Build each version of your game from unity (This is the time consuming part)
- webgl and windows are straightforward
- linux requires you create a .x86_64 file, name this after your game.
- osx requires you create a *.app folder. Put this in the osx folder if it is not after building.
- Run each of the 4 commands
- On itch, change the webgl build to 'run in browser'. The other 3 builds will be automatically tagged weith the correct platforms.
The results should how your entire upload history like this (The post compo uploads are only bugfixes)

WebGL
Target WebGL from the start! It is the most accessible platform and requires the least amount of work for players to start. Reduce the friction of getting into your game so you get more plays and more feedback.
Providing other builds is also helpful, but IMO WebGL is by far the most important.