Found this on another forum.
Voltage and Cell Count:
LiPolys act differently than NiCad or NiMH batteries do when charging and discharging. Lithium batteries are fully charged when each cell has a voltage of 4.2 volts. They are fully discharged when each cell has a voltage of 3.0 volts. It is important not to exceed both the high voltage of 4.2 volts and the low voltage of 3.0 volts. Exceeding these limits can harm the battery.
The way to ensure that you do not go below 3.0 volts while flying is to set the low voltage cutoff (LVC) of your electronic speed control (ESC). It important to use a programmable ESC since the correct voltage cutoff is critical to the life of your batteries. Use the ESC's programming mode to set the LVC to 3.0 volts per cell with a hard cutoff, or 3.3 volts per cell with a soft cutoff. If your ESC does not have hard or soft cutoff, use 3.0 volts per cell. You will know when flying that it is time to land when you experience a sudden drop in power caused by the LVC.
If your ESC has an automatic lithium mode. Use it, it will correctly sense the number of cells and set the auto cutoff appropriately.
If you have previously been flying with NiCad or NiMH batteries, switching over to lithium polymer will result in a different number of cells being used. If you had 6 to 7 round cells then 2 lithium polymer cells will correctly duplicate the voltage of those cells. If you had 10-11 cells then 3 lithium polymer cells would be right for you. There are a lot of 8 cell flyer's out there that are stuck between 2 and 3 cells. In my experience the best option is to determine how many watts you were using before and duplicate that with your LiPos, Motor, and Prop. For example. If you were running 8 cells (9.6volts) at 10 amps on a speed 400 airplane, then you have 9.6 x10, 96 watts. So if you went with 2 lithium polymer cells (7.2 volts nominal) then you'd need to change your prop such that you used 13 amps. If you went to 3 LiPoly's (10.8 volts nominal) then you'd need to reduce the amperage to 8.9 amps. These estimates are approximate, and some experimentation is required for best results but conserving Watts is a good way to start
Here's the link to the full guide, maybe it'll give you some answers.
http://www.rcgroups.com/forums/showthread.php?t=209187