Auto will recognize the wherever it want to use GPU and CPU. but we'r not sure whether its optimize the processing in a well manner.
Note: In the iPhone OS publish settings dialog box in Flash Professional CS5, there is a rendering selector that includes Auto, CPU, and GPU. When GPU is selected, some rendering operations will be GPU-accelerated—generally those that make use of bitmap operations. If CPU is selected, no GPU rendering will be used. Select CPU mode only if you encounter behavior, performance, or compatibility problems when running in GPU mode.
http://www.indieflashblog.com/understanding-gpu-rendering-in-adobe-air-for-mobile.html