There is a very good explanation on how to work with repositories via the desktop GUI at https://help.ubuntu.com/community/Repositories/Ubuntu
This would be the preferred method for newer Ubuntu users.
If you'd prefer to manually edit the files containing repositories, everything you'd ever want to know can be found at http://manpages.ubuntu.com/manpages/zesty/man5/sources.list.5.html
As a starting point and to directly answer your question, /etc/apt/sources.list is the file that contains your repos. There is also stuff in /etc/apt/sources.list.d
Usually, error messages will specify specific repositories that cannot be found by apt update. In that case, you'd edit out that repo from sources.list
The repositories for unity-tweak tool can be found at https://launchpad.net/~freyja-dev/+archive/ubuntu/unity-tweak-tool-daily
If you installed unity-tweak from source or as a Ubuntu package, you'd upgrade it by doing a download from https://launchpad.net/ubuntu/xenial/+source/unity-tweak-tool