Debian uses Quilt system for per-package patch maintenance. While packaging a software you get the original source (i.e. orig.tar.gz), and add patches on top of it with Quilt, and build it that way.

Then you run the tests, and if they pass, you package and upload it.

This allows a patch(set) can be sent to the upstream as a package saying "we did this, and if you want to include them, this apply cleanly to version x.y.z, any feedback is welcome".