Meteor offers some special folders that can help the developers’ in structuring their apps.
Files from this folder will only be run on the server side. This is the place where methods, Meteor.Publish() functions, and other sensitive data should be held. All of the authentication data should be held here. You don't need to use Meteor.isServer() for the files inside this folder.
This is the place where you should place your images, favicons, and all the other data that is served to the client.
Files from this folder can be accessed only from the server. They will be hidden from the client. You can put JSON or EJSON files that only the server will use inside this folder.
The rest of the folders can be structured the way you want. The code that is placed outside of the folders mentioned above will be executed on the client and the server side. This is a good place where you can define your models.
It is always good to know load order of the files. The following list is taken from the Meteor Official Documentation.
HTML template files are always loaded before everything else
Files beginning with main. are loaded last
Files inside any lib/ directory are loaded next
Files with deeper paths are loaded next
Files are then loaded in an alphabetical order of the entire path