Thats whats so much fun! You still shift it, just instead of moving the lever you tap up or down. You still can have full control of the clutch. I have a solenoid in the clutch line so it wont re-engage the clutch until the shift is complete. So to shift you tap any volume button (this arms the system) then I have an optical encoder on the clutch pedal. The shift doesn't happen until the encoder is happy with clutch position at which point it "holds" the clutch line pressure with the solenoid, shifts then releases the clutch.
So you still have all the "feel" of a real manual gearbox, but with quickest shifting possible