The bars represent how much your secondary attack must be charged before being able to be used. A long bar must be charged to full before being used, and can only be used once before having to be charged again. The smaller bars only need one of the bars to be filled before being able to be used, and several charges of the attack can be stored, as only one bar is used per secondary attack.
They also are representative of the general strength of the attack. Attacks with many smaller bars deal significantly less damage per attack, but can be used more frequently, and larger bars hit much harder per attack, but take much longer to be charged.
Also, the damage amount listed to the right of the move is calculated per bar, and not split between them. The bars simply represent the amount of uses that can be stored, and how much charge is needed per use. The damage is therefore per use.