Okay, here's how to use it.
Export your game with nw.js and place Launcher.exe and Game.exe in the win32/64 folder.
Run Launcher.exe and select a resolution and screenmode. Then press either launch or exit, in both cases your choices get saved. After pressing launch the game will run with your choices applied. If you want the 'window' choice to work though, you'll need to set up some events at the start of your game like I've done in the test.capx example.
If you've run the launcher once and don't want to change resolution or screenmode again you can just run Game.exe directly with your saved settings.
EDIT:
Oh, and you need to turn kiosk mode off in build settings or you won't be able to cancel fullscreen in C2.
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Quick breakdown of what the different cfg files do:
launch.cfg:
Used by Game.exe to get the name of the executable (nw.exe), the desired resolution to run in, the delay in seconds before switching to the desired resolution, and the time in seconds to display a black background while the game loads. (The last one doesn't work properly so I'd leave it alone for now.)
You should only change "nw.exe", and the two last lines in launch.cfg. The resolution values get overwritten every time launcher.exe gets run so there's not much point changing those.
mode.cfg:
fullscreen/window toggle. 0 = fullscreen, 1 = window. Set by launcher.exe. Read by Game.exe (tells it not to switch resolution in window mode) and by your nw.js build (check out the capx to see how).
osH.cfg/osW.cfg:
Reference values. Allows C2 to read the resolution selected in launcher.exe. Best not mess with these.
osDH.cfg/osW.cfg:
Same as above but for system resolution.
res.cfg:
This is the file where you set up all the different resolution choices you want to make available to the player.
ui.cfg:
You can set your own names for launcher.exe's window and buttons here.