D&D Encounters is play of the first sections of the current storyline adventure at a game store on a Wednesday. Stores which create D&D Encounters events get sent a PDF of the first sections of that adventure, which has a few small tweaks to help it to fit into the Encounters programme, primarily a cap on XP available each session so that over the course of a few weeks new players can join, or players can miss a session, without falling too far behind.. So for the first season, DDEN was the first three chapters of Hoard of the Dragon Queen. There was no explicit division into 2-hour sessions, though there's a note that recommends running it in sessions of about that length. Rise of Tiamat (and the later sections of HotDQ) are not technically part of Encounters - though stores may run those on Wednesdays alongside tables of Encounters (if they've a fresh group of new players or players who'd like to try out a different character and play the first parts again).
It's possible to play Hoard, etc, outside the Encounters structure but within the AL. Technically stores should report this using the Casual Play event as it isn't Encounters or Expeditions, but this doesn't change the AL status of those games. One challenge of that in a store is that players need to start with 1st level characters so it is useful to be able to offer the Encounters early episodes as well as running higher level adventures.
There may be some tweaks to this as the new season begins, with more information anticipated in the next version of the ALPG and the new Encounters PDF, due early March.