Hopefully this achievement is relatively straight forward. If you're having trouble make sure you've equipped the right auxiliary (proton bombs) and make sure you're dropping them when you see the green downwards arrow icon that flashes when you're right above an enemy capital ship. You need to drop them either on an unshielded capital ship, or by flying under the blue shield and dropping them then. They need to land on undamaged sections of the ship as well, as it won't count if they're dropping on an already destroyed section.