Special bonuses are added to the damage:
Example: 1-3 damage + 2 special damage.
If the roll is 2 for the damage then:
2 damage + 2 special damage= 4 damage HOWEVER........
Please note that this is only a PART of the battle formula. This does not mean that the unit will always do at least 3 damage(in the example from above). Oher factos can modify the results under 3 and above 5.
Sorry to be vague about the battle system. In conclusion special bonuses generally increase the constant damage.