The first thing you need to know when structuring your apps is that the Meteor tool has some directories that are hard-coded with specific logic. At a very basic level, the following directories are "baked in" the Meteor bundler.
client/ # client application code
client/compatibility/ # legacy 3rd party javascript libraries
imports/ # for lazy loading feature
lib/ # any common code for client/server.
packages/ # place for all your atmosphere packages
private/ # static files that only the server knows about
public/ # static files that are available to the client
server/ # server code
tests/ # unit test files (won't be loaded on client or server)
Reference page: Meteor Guide > Special directories