It's really easy:
– In the "Pop over position" section, set left to "50%" and top to "50%" too.
– In the "Pop over margins" section, set the left to (negative) half the width of your popup, and top to (negative) half the height of your popup. That is, if your popup is 800×600, then set the left margin to -400px and the top margin to -300px. The remaining margins are set to 0.
Attach a screenshot with my values, and my website (http://www.papaenapuros.com/) to see the effect.
Hope you find it useful.