I sat down last night and this morning to nail down the content of COT2 Book 1 (the first four stories) and ended up doing the same for 2 and 3 as well, though in much less detail. In the end I went with a more chronological arrangement (though not a strict one) where the first four stories concern events that actually happen before COT, dealing with new characters, with some cameos. They'll all be very different, some very dark, some more lighthearted, some very independent, some very fanficcy, some taking place over the course of months, some hours. The second book will be a direct continuation from the end of COT, and in the third book the various short stories will start to come together into a larger plot, with the characters and events from the first book tying in with the second.
It's possible that for books 4, 5, and 6, I may switch back to more chapter-like stories, with a continuous flow. It depends on how things go! I suspect it may be wise to wait until these twelve stories are written before planning out the next twelve. I will say one thing is certain - going with a short-story format has made things much easier to manage.