Bonuses are groups of territories that give you an income bonus if you control all of them. The bonuses value is typically placed in a small rectangle near the bonus, the so-called bonuslink, but other shapes are used as well.
The basic value of the bonus is determined by the map creator. Many map creators value their bonuses by the number of territories that make it up; the more territories in the bonus the more armies are awarded per turn. Also factored into how many armies are awarded by a bonus is how exposed it is. Generally, if a bonus is in the corner of the map with few access points, then it will be worth less than one that has the same number of territories but more access points. There are also special bonuses that only contain one territory, capitals for example. These should not be worth more than 1 or 2 armies, or it may get unbalanced.
In the settings you can change the value of a bonus to anywhere between 1000 and -1000 when making your own game.