Create packages
Of course not everything fits in this approach, but in large apps you'll have a lot of functionalities that can be isolated.
Anything separable and reusable fits in packages, the rest goes in the usual directory structure, as mentioned in other answers. Even if you don't make packages to avoid the overhead, structuring the code in a modular manner is a good idea (see these suggestions)
Meteor allows a fine-grained control over how you load your files (loading order, where: client/server/both) and what the package exports.
I especially find very handy the easy way to share the logic between the related files. Say, for example, you wanna make some util function and use in different files. You just make it "global" (without the var
) and Meteor will wrap it in the namespace of the package, so it will not pollute the global namespace
Here's the official doc