I have used the Power Trainer before so I know how it works. Replace one skill with another.
I had just made Commander and can now use the second power of my Engineer BO at my console.
I took him to the Power Trainer and went to replace his Boarding Party 1 with Reverse Shield Polarity.
Instead of replacing the skill it stacked the Reverse Shield Polarity 1 Skill UNDERNEITH the Boarding Party 1 skill leaving me with both skills and no way to use Reverse Shield Polarity, or get rid of Boarding Party 1.