The game's host can setup the timer by clicking the button in the top left corner:

You can play as you've been used to, without a timer. But if you decide to use it, you can choose among the three possible modes:

Manual - Simply click the timer when someone thinks for too long.

Automatic for side - The time is shared by the whole team, and it is up to them how much of it they use for clues and how much for guessing.

Automatic for role - It allows you to set a different time for operatives and for spymasters.

If the time runs out, the game does not switch to the other team automatically. It is up to you how to solve the situation, just like when playing on a table.