If you have one 25% Set A (Cat1) bonus, and one 25% Set B (Cat2) bonus, you would receive a 1.25x final damage multiplier from Set A, and a 1.25x final damage multiplier from Set B. For example: if you have two +25% Set A (Cat1) bonuses, you would receive a 1.5x final damage multiplier from Set A.
Most bonuses fall within one set or the other, which determines the order of operations for calculating damage: like bonuses are added within their set, which determines the category's final bonus, which is then treated as a final multiplier. Damage bonuses in Star Trek Online are neither straight additive, nor strictly multiplicative - there are two distinct 'categories,' or 'sets,' of damage bonuses.
