I guess the question explains it all...
This really depends on the type of bug or wishlist item you with to report. There are two aspects to unity. There is the upstream source and the Ubuntu package.
The upstream source is basically what you can find at https://launchpad.net/unity. It is the unity application itself. This does not include any Ubuntu-specific changes that we might ship or the deb package.
The Ubuntu package is the deb version of the upstream source that you can install from the Ubuntu repositories. This can be found at https://launchpad.net/ubuntu/+source/unity. The package takes care of installing dependencies, installing all of the files from the upstream source into the correct locations, and making any Ubuntu-specific changes that need to be made (among other things).
If your bug or feature request has to do with the application itself (i.e. some feature does not work properly, a request for new functionality, etc.) you should file it against the upstream application here.
If your bug is an issue with the Ubuntu package (fails to install from repositories, missing dependencies, Ubuntu-specific features not working, etc) you should file it against the Ubuntu package. This guide will guide you through the process of using
Since unity is not currently synced from Debian, you do not need to worry about reporting the bug there.