The air lining in the 2 liters doesn't come into contact with the actual yeast/sugar mixture right? I read it is supposed to be a few inches above the actual liquid. (Please correct me if I am wrong)
You are correct.
This lining doesn't connect to the tank straight, so do I need the check valves between the 2 liters and the separator bottle or can I just place one between the separator bottle and the lining into the tank?
I used to only use one check valve (between the aquarium and the separator bottle).
Hope this helps,