My understanding is that most of the time you would want the FINAL ROLLOUT value. So you would use the second gear ratios for the calcuations.
I use the rear tires to calculate the rollout. In most cases, you are using a tire split that would create a 1:1 (or close to it) final drive ratio, because of the pulleys that make up the transmission. Also the rear tires are typically bigger and are what will be "driving" the car (more distance per rotation).
Below is a link to some good articles regarding transmission, rollout and overdrive calcuations.
http://www.tsrcar.com/garage/paddock/paddock.htm
Doug