You create a directory called packages and clone the package you’d like to modify into it. Meteor would then start reading from this local fork instead of its atmosphere counter part. You can then modify it however you want and then create the PR back into the original package.
The repo is the package (plus some extra files and folders such as demo folders and github related files and folders such as docs, CODE_OF_CONDUCT which you don’t need to remove although you could.)
To make sure you use a local version of it in your Meteor app, you can increment the version number in package.js and check the version under app/.meteor/versions