Skyhold can be customized in a variety of ways to best reflect the style and priorities of the Inquisition.
To complete the quest you simply need to find the Undercroft then customize Skyhold.
From the point where you re-gain control of your character, turn around and go through the door at the end on the right to find the Undercroft.
Interact with the Skyhold Customization work bench to complete the quest. You don't actually need to customize anything though there are some options available even before you unlock more.