Initially, you're given the option to pick "Upload the code" or "We're letting the geth die". Similar to Virmire, this is actually a false choice; it doesn't matter what you pick here, the true decision comes immediately afterwards.

Can you save Tali and Legion?

To save the two races, choose either the Paragon or Renegade option, which will tell Legion to upload the code while Shepard convinces the Quarian fleet to stop their assault on Geth ships. Tali and Admiral Koris backs Shepard up, and the firing stops with both the Quarians and Geth finally brokering peace.

Should I save Admiral Koris or the civilians?

Letting Koris die is costly: Admiral Koris' leadership is lost and, if the quarians survive the entire ordeal, their Civilian Fleet panics without him. Whatever your choice, you will mount a turret inside the shuttle and provide cover fire for whoever you are rescuing.