To configure keyboard shortcuts through the JSON file, open Keyboard Shortcuts editor and select the Open Keyboard Shortcuts (JSON) button on the right of the editor title bar. This will open your keybindings.json file where you can overwrite the Default Keybindings.
Open Keyboard Shortcuts JSON button
You can also open the keybindings.json file from the Command Palette (⇧⌘P) with the Preferences: Open Keyboard Shortcuts (JSON) command.