Say I cast fireball using Twinned spell, I would expend 3 sorcery points and cast a second fireball, would casting those two fireballs use one or two of my level 3 spell slots?
Using Twinned Spell only uses one spell slot. This is because you are not casting two spells, rather you are making a single spell hit more than one target.
"...target a second creature in range with the same spell..."
However, it's worth noting that you can't cast Fireball with Twinned Spell.
Quote from PHB page 102 (emphasis mine)
Twinned Spell: When you cast a spell that targets only one creature and doesn’t have a range of self, you can spend a number of sorcery points equal to the spell’s level to target a second creature in range with the same spell (1 sorcery point if the spell is a cantrip).