Hi there,
I desolder them using a special soldering tip, a 1cm blade to heat up both pads a the same time.
Then I gently clamp the MB in a vise so it stands up vertically.
Next I put a small conical solder tip on the component side and place the desolder gun on the opposing pad. The moment the solder tip sinks into the top pad I wait about 2s long and then engage the desolder gun. I pull away the solder tip from the top pad and immediately after the desolder gun.
That should leave a nicely cleaned hole.
Also be careful. Some MB use a reverse silk print, as in, the filled half circle can be the positive instead of the negative.