Secure the motherboard so you can access both sides of it.

Use the soldering iron to heat one side of a through-hole.

Use a desoldering pump on the opposite side of the through-hole to suck up any remaining solder.

Don't heat the through-hole continuously for longer than 15 seconds at a time to avoid damaging the pad.

If needed, use solder wick to remove any residual solder.

Repeat this for all through-holes and both sides of the motherboard.