Arduino IDE with AVR instruction set

I need to use AVR instruction set in Arduino IDE for specific functions. Where do I find the documentation for the same. example how do I set the Timer , Check the Timer overflow status, Reset the Timer flag etc.

The chip is fully documented in its datasheet. http://www.atmel.com/images/Atmel-8271-8-bit-AVR-Microcontroller-ATmega48A-48PA-88A-88PA-168A-168PA-328-328P_datasheet_Complete.pdf