First off:
A Counter Attack can happen any time the Attacking Faction has at least one win on a planet. If the Attacking Faction has 11 wins, all defenses on that planet will be Counter Attacks until the Defending Faction wins a point back.
A Counter Attack is triggered when the Defending Faction has 12 players queued up to Defend before the Attacking Faction has 12 players queued up to attack (i.e. the first team with a full 12 is going to Attack/Counter Attack). It has absolutely nothing to do with the number of wins the Attacking faction has on the planet (except in cases as noted above). Russ confirmed this on Twitter.
Second:
When you're in a lobby, as soon as your whole team is shown in the lobby, there is a Header Bar at the top of the lobby window that tells you if you're Attacking, Defending, Counter Attacking, or Holding Territory (which is defending as the Attacking Faction). This means you have at least 1 full minute to edit your drop deck accordingly, which you can do directly in the Lobby.
(Note: This process may change soon. You may want to watch Russ' town hall meeting on Twitch tonight to hear about future changes.)
Finally:
When a Defending Faction successfully Counter Attacks one point is removed from the planet's Attacker Wins.
I am 100% positive about this information, and I hope this helps you all understand Counter Attacking better.
Edited by DEMAX51, 16 December 2014 - 05:09 PM.