During the development of GitTorrent, I was being asked questions that led me to realise that there wasn't a very good overall view of how the various proposed GitTorrent messages fit together to make fetches work.
So, I've written a whole lot more on this with a few paragraphs which I hope will pull it all together. If you found the RFC previously indigestable, try reading:
http://gittorrent.utsl.gen.nz/rfc.html#peer-wire-guidelines
If there are parts which still aren't clear, please ask questions and I will aim to write more clarification to the specification.
Cheers! Sam.