Ok, there is a new version coming so I will comment based on that. Apple takes about a week to approve it, so you should get it by Friday the 10th or early the following week.
OK, first the Final Drive Quick tune - The idea is that it find the best final drive for your power profile based on the HP, Torque, and adjustable range. So, you type in the HP, Torque, and MINIMUM final drive. Then, it plots a point in your range that should give you the best access to power. You can adjust the transmission either by using various tranny tricks first, then setting the final drive OR you can set the final drive first, then adjust the transmission. For the MOST part (but not always) I prefer to adjust the final drive first, then adjust top speed and let the game pick my gears. For High torque engines, I set the final drive all the way to the right, the top speed all the way to the left, then I set the final drive. That helps with wheel spin.
So, for you car, You should end up with 3.559 as a final drive. I would set the final drive first, then adjust the top speed as needed, then slide all the gears to the right for max acceleration.
For the ride height - Originally, I had reverse rake for front heavy cars and positive rake for rear heavy cars. The version you have has a positive rake method (so lower int he nose than in the rear) for ALL cars. I have been testing ever since and found that I was wrong and the new version (2.0.8) is going back to the reverse rake method, but this time, for ALL cars. I am gaining time everywhere.
So, to answer your question, you set the front to the value the app gives you and set the rear the same way. In your version, you would get about 15 mm more in the rear if you had a FR layout. The new version reverses that. You can try it with your version by just reducing the ride height values for the rear. I found that FF cars really love having the rear end almost bottomed out. So, for the Audi, I think it's 50/50 (correct?) so use the middle of the adjustment range to get your front end values. for the rear, adjust it to about 10-15mm lower than the front.
I also totally forgot to invert the front toe values from WAY back in version 1.01 of the game. I finally fixed that now.
Try the new app results against the old one. I think you will find some gains.