This is how I've set my first and second level protection voltage thresholds. I found the default setting with 14.8 Volts in the 'No Load' without any value in the 'Loss' field meant the Second Level Protection kicked in far too early and the Quad became sluggish to ascend. Even at full throttle, it would only rise very slowly. Flicking it into manual mode and the Quad would take off like a rocket. That tells me the battery has plenty of juice left in it but the Naza is artificially limiting the maximum throttle available by slowly moving the mid-point up.
The results from the Eagle Tree logger show a loaded voltage level throughout the entire flight. 14.4 and 14.2 is probably a bit conservative but I'll test it out and see how it goes. I reckon I might change it to 14.2 and 14.0. We'll see.
****Update - 5th July 2012
I think these values are too conservative. On the last flight, 2nd level kicked in and I still had about 50% left in the 2650mAh 4S. I've set them to 14.2 and 14.0 (zero loss) and will do another test flight. The Eagletree logger is fantastic for this type of problem.