Press K to get your skill box up, and at the bottom right you should see a Skill Empowerment button. Click that, and another box pops up. Click and drop the skill you want to empower into the square box, and click the up and down arrows to put in different empowerments.
You can roll your mouse over the skill in the box to check what adding a skill points does to the skill, so you can play around with skill points before pressing Confirm. Once you pressed confirm, the skill points are used and you can't go back.
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