i'm not sure I understand your problem, your post is very difficult to read for some reason ... did you type it on a cell phone or some other device with a very small screen? and why is it double spaced?
anyway ... a good Lion or LiPo charger should be fully automatic, no microcontroller required or desired even... to leave such things in the hands of firmware could result in a catastrophy. From my quick read of the datasheet, your chip is fully automatic, and doesn't require a microcontroller to manage anything. Their i2c interface only provides a few basic commands, hardly worth the effort in my humble opinion.
I recommend starting with something a bit simpler, such as Maxim's MAX1551, MAX1811 or MAX1898. Analog Micro also has a simple LiPo charger similar to the 1811.