The Team Base is used for Capture The Flag game mode. When played, the flags will appear on it.
In it's properties, you chose it's team color. You can have only one red base and only one blue base per world file.
Note that when using it , you also have to tell the Level that it exists, to do that, press 'N' and find the "World Info" entity in the list , select it and press enter. Now highlight "Red team Base" and "Ctrl+Alt" on the "Team Base" you have set to red. Do the same with "Blue team Base".
Also note that the "Team Base" isn't a spawn point, so you 'll have to add those as well.