I'm not quite sure which clock you're talking about but I'll try my best to explain all of them based on what I gathered from playing in real time.
For this example I'll be using the game Time masters.
Starting off with the lobby timer:
On the left hand side you'll see something similar to this displaying how long the game is estimated to take

The time displayed will differ depending on several factors, such as how long the physical copy of the game takes, the number of players you are playing with and the game's complexity.
While a game room is being filled in, you're given 7 options to set the pace of the game and while how much time you get differs slightly for each game, They are as follows:
Realtime - Fast Paced : Game usually starts with 1-2 minutes to make your moves
Realtime - Normal Paced : Game usually starts with 3-5 minutes to make your moves
Realtime - Slow Paced : Game usually starts with 5-10 minutes to make your moves
Turnbased - 2 moves per day : You probably start out with around 1440 minutes to make your move.
Turnbased - 1 moves per day : You probably start out with around 1440 minutes to make your move.
Turnbased - 1 moves per 2 days : You probably start out with around 1440 minutes to make your move.
Turnbased - No time limit. : You probably start out with around 9999+ minutes to make your move.
You'll also be told the pace of the game just before starting when confirming your participation to the game

as displayed in the above image , all players will start with 5 minutes and gain an additional 30 seconds at the start of each of your turns.
Lastly while you're in game you'll have the in game timer on the right hand side just besides your name.

This timer will count down whenever you are required to take an action and stop counting down once you're done. If you're taking too much time or it goes in the negatives the timer will end up turning red instead and start counting up. You'll generally be marked as a slow player when that happens.
I hope that explains it for you, or whatever Een said works out.
For this example I'll be using the game Time masters.
Starting off with the lobby timer:
On the left hand side you'll see something similar to this displaying how long the game is estimated to take

The time displayed will differ depending on several factors, such as how long the physical copy of the game takes, the number of players you are playing with and the game's complexity.
While a game room is being filled in, you're given 7 options to set the pace of the game and while how much time you get differs slightly for each game, They are as follows:
Realtime - Fast Paced : Game usually starts with 1-2 minutes to make your moves
Realtime - Normal Paced : Game usually starts with 3-5 minutes to make your moves
Realtime - Slow Paced : Game usually starts with 5-10 minutes to make your moves
Turnbased - 2 moves per day : You probably start out with around 1440 minutes to make your move.
Turnbased - 1 moves per day : You probably start out with around 1440 minutes to make your move.
Turnbased - 1 moves per 2 days : You probably start out with around 1440 minutes to make your move.
Turnbased - No time limit. : You probably start out with around 9999+ minutes to make your move.
You'll also be told the pace of the game just before starting when confirming your participation to the game

as displayed in the above image , all players will start with 5 minutes and gain an additional 30 seconds at the start of each of your turns.
Lastly while you're in game you'll have the in game timer on the right hand side just besides your name.

This timer will count down whenever you are required to take an action and stop counting down once you're done. If you're taking too much time or it goes in the negatives the timer will end up turning red instead and start counting up. You'll generally be marked as a slow player when that happens.
I hope that explains it for you, or whatever Een said works out.