Narrow, 3 part bar above battle bar

After Haven was buried in the avalanche and you were in the underground cave, a new gameplay mechanic was introduced-the special ability. You could now use the mark on your hand to generate a destructive area of effect spell. If you look under your tactics menu, you will see a new skill tree for this.

The new bar you are talking about is a power bar (called focus). Once you charge at least one level you can use your special ability (doing damage charges the bar). The other 2 bars cannot be filled until you upgrade them with inquisition points (under Cullen's Forces section). Once you unlock a specialization, it will draw from the same focus bar. Your companions will also get special abilities (they unlock specializations as soon as the inquisitor does). They also draw from the same focus pool.

With more focus bars used, the special abilities become more potent (so more destruction, or longer protection or higher defenses etc). The special abilities in the specializtion trees have descriptions of what the different levels do.