Can I monitor an ATmega406 using an Arduino Uno via SMBus?
In my opinion your best bet would be to use Atmel Studio 6.

And here you can find details about the Atmega406 itself

http://www.atmel.com/Images/Atmel-2548-8-bit-AVR-Microcontroller-Battery-Management-ATmega406_Datasheet-Summary.pdf