The options for managing your Twitter API are under Settings > Twitter Updates.

TweetDeck offers you 2 options for managing your API usage.

Option 1 - Automatic

This option is the default for all new users and should not be changed unless you are an advanced TweetDeck user.

By selecting the option to Allow TweetDeck To manage my Twitter API limit, you will allow TweetDeck to monitor your API usage and adjust the rate at which you are using it accordingly. This should mean that you are far less likely to run out of API calls as TweetDeck will adjust refresh rates dynamically. This will lead to a balanced use of your API and should make for a better experience using TweetDeck.

Essentially, every time TweetDeck makes a call to the API it checks what your remaining limit is. Using this information, combined with the time remaining before the next reset, TweetDeck adjusts your refresh rates automatically to ensure you will not run out. 

Depending on your API usage so far in this current hour, TweetDeck will intelligently speed up or slow down your update rates to compensate, thus ensuring you never see the dreaded "Rate Limit Exceeded" message.

Using this option is HIGHLY RECOMMENDED.

Option 2 - Manual adjustment - ONLY RECOMENDED FOR ADVANCED USERS

Deselecting the option to Allow TweetDeck To manage my Twitter API limit, allows you to adjust the amount of API calls that TweetDeck should make for each type of feed.

The rate at which the different tweets arrive is governed by the 5 sliders

These sliders represent the 5 types of feed that TweetDeck receives: All Friends (which also populate Groups), Mentions (Replies), Direct Messages, Lists and New Followers.

Moving the slider changes the % of the API limit you wish to use in collecting each type of feed. As you adjust the %, you will notice the refresh time changing over on the right-hand side of the slider. This indicates how long it will be between each ‘batch’ of new tweets in this category.

If your tweets are not arriving quick enough try adjusting these settings. Best practise suggests keeping your total around 80%.

If you set your API levels so the total is above 100% you will find you run out of calls before the hour is up, thus leading to the "Rate Limit Exceeded" message.

You can keep track of your API usage by hovering over the column navigator at the bottom of the screen.