Like other champs that have CC based on a skill-shot, use it aggressively pre-6, and then afterwards you need to save it. Kassadin doesn't have much sustain or staying power, so if you can force him out of lane to get a minion/exp advantage, do it.
As I said in the thread about the person asking about Ahri tips, Kassadin can restore mana but only when he autoattacks minions. If he's low on mana, harass him and don't let him near them. This will stop his inflow of extra mana, pacing the game to your needs.
After 6, save your Q for when he jumps at you. Like Yi or Pantheon, when Kassadin jumps at you, it's a clear indicator of where he's going to end up since he wants to be relatively near you. Fire and quick detonate for the stun, flash frost, and go to town on him-- or use the stun to get away.
At low levels, Kass won't really be able to DPS through your egg form easily, not without jungler / tons of minions helping. Feel free to be a little more aggressive than usual, but don't forget to be aware of ganks and mia's.