If you want an overview of how VS Code differs from traditional TextMate clones, read Orta's post on the Artsy blog.
Ideally you should run Metaphysics
This repo uses babel at runtime via require('babel-core/register'); and so there are no source-mapping files, this means that VS Code does not support LOC breakpoints from your source code into the real transpiled code in Metaphysics.
You can work around this though using the debugger function inside your source code instead.
To start the debugger, run the debugger (VS Code defaults this to f5, I typically re-bind this to cmd + r) and the bar at the bottom should turn orange. Then in the LOC you want to debug inside, add debugger;. This will open the transpiled source code, and on the left in the debugger menu you can see all of the state, and the console should work at the bottom.
You can also open a new tab with about:inspector in Chrome and it will provide a button to load up the chrome inspector in Chrome Dev Tools.
There is more information about using VS Code, with terminology and keybinding recommendations, inside the Emission repo.