If you want to override/change anything, you can just do it with the same name of the file, through Monkey Patching. Some real world examples of this method:
If you want to extend Decidim, the preferred way should be by having a Module. This is a Ruby on Rails Engine which provides ruby code (models, views, controllers, assets, etc). You can use it in multiple ways:
Putting it on the same directory as your app and pointing on the Gemfile. See example on GitHub. For instance:
gem "decidim-debates", path: "decidim-debates"
Publishing on a git repository and pointing in on the Gemfile. For instance:
gem "decidim-initiatives", git: "https://github.com/example-github-organization/decidim-module-initiatives"
Publishing it on rubygems.org
You can learn more about Modules in the development guide.