You can use a bootloader to download a program to the MCU via UART but it is easier to just use a dedicated programmer. 

AVRISP mkII In-System Programmer - http://www.atmel.com/dyn/products/tools_card.asp?tool_id=3808

If you have Ubuntu installed, all the GNU AVR tools can be found in the package manager.

Other Resources:

A C library to program various number of ATmega chips as well as abstract interfaces to set up timers, drive servos, read sensor data, etc..