Coda really shines when you need to edit files directly on a remote server (which makes sense, because Panic is also the maker of Transmit). This is primarily when we use Coda in our shop. Although the time spent in remote files does get tracked, it's always tracked under "Unknown Project". There is no way to create rules because the files are in Coda's cache using random strings.
/Library/Caches/Coda 2/6A1F954C-35E2-45C9-A923-4E42A35E1040/server.js
/Library/Caches/Coda 2/E29824C3-49A5-4217-B5FB-3196FC792999/server.js
/Library/Caches/Coda 2/64DC0FB3-2C57-4D19-A94B-BC1AD6F21B94/server.js