While Pharynx remains head of the military branch of the Changelings, Tempest Shadow becomes the head of the guard for Twilight's castle. She not only commands the pony guard, but the Storm King's formal henchmen as well. Grubber is still around, he becomes the head chef of the castle.
Tempest not only is the head the guard, but prides herself as Twilight's personal body guard during out of town meetings. This is how she met Pharynx, who was with Thorax for one of these meetings. The two didn't hit it off right away, but talking about past battles and strategies brought them a little closer. In time a long distance relationship takes place.
I would imagine the two aren't very showing of their relationship status, being official around each other in the public eye, yet friendly and casual when alone. The two enjoy testing each others strength and battle styles against one another. Tempest Shadow has a tendency to get the best of Pharynx and he finds himself pinned to the ground with his beloved grinning down triumphantly at him.