This is a fairly broad and opinionated topic, so I will try to give a concise answer that relates to matters discussed in the Meteor Guide.
First, I would follow through with the tutorial to get its purpose. To me, it seems that it is not intended to teach you how to build a complex app, but rather to get the hang of React in a basic Meteor project.
There is no definitive answer to the question of project structure, as it is fairly opinionated. Some partition by function, others by feature; some like deep nesting and some prefer a more flat structure.
The main theme is that the modules' explicit import syntax makes your dependencies explicit and therefore prevent the need for guesswork or awkward filenames that loses semantics and makes finding the source of each symbol a non-trivial task.
The app structure tutorial is not complete either and mainly includes guidelines.
Let's assume something like the following simple structure, that fits pretty closely with the use-case:
.
├── client
│ └── main.js
├── imports
│ ├── api
│ │ ├── api.js
│ │ ├── api-server.js
│ │ └── module1
│ │ ├── collections.js
│ │ ├── methods.js
│ │ └── server
│ │ └── publications.js
│ ├── client
│ │ └── index.js
│ └── server
│ └── index.js
└── server
└── main.js
Anything in the imports directory is not automatically imported. It all starts in the server/main.js and client/main.js entry points.
They, in turn, import the imports/<target>/index.js, which is where the app is bootstrapped for each target (client/server).
Since some of the api code is server-specific, you would probably want to create a server-api.js file or the like that also imports the server resources.
During the bootstrap process, the server's index.js will
import '../api/api-server';
api-server.js will:
import './api';
import './module1/server/publications';
while the client/index.js could import api.js directly.
Standard methods and publications do not export any symbol, so no need to import them individually, but only the file that they are defined in.
api.js will:
import './module1/methods';
where methods.js and publications.js will import the collections.js file, assuming they need it.
Again, this is a very broad and opinionated topic and there are several ways to structure your project.