You'll automatically be able to step through the server code, only it's packed into the application package.
You'll need to set a breakpoint in a call after meteor.startup, like this:
Meteor.startup(function() {
debugger;
return Match.test('3', String);
});
Most of the server code is in this path:
"(your project dir)/programs/server/packages/'
in the debugger.
But you'll have to wait til Meteor.startup(), because otherwise all the sources won't be loaded.
The code may not exactly be structured like in the meteor repository, but you should be able to compare it with the packages/ - folder in the meteor repo.
If you want to edit / change a meteor package temporarily to change something for your specific project, you can clone the whole meteor repo somewhere and only copy the package you want to override to your packages/ - directory, meteor will load it from there then.
Also I have an issue right now in the debugger coming with meteor that I can't click on folders in the "sources" - browser, but I can focus it via mouse click and then navigate it with the arrow keys... :)
Best wishes
Daniel