Seasoned AVR programmers or those who aren't so keen on the minimalist Arduino IDE will find this tutorial interesting. Omar Francisco has simplified a tutorial on how to use Atmel's Studio 6 IDE to program Arduino boards by creating an installation script that takes care of most of the setup for you. Then he continues to describe how to create new projects and Arduino libraries in the IDE. Using Studio 6 is also a good idea if you're looking to transition from the Arduino to raw AVR or ARM Cortex work, as you can gain familiarity with the software now and reduce your learning curve when changing platforms.
If you are new to Arduino, join in with our range of Arduino-compatible hardware, prototyping shields and module range. A good start is the Freetronics Eleven, the Arduino Uno-compatible board with onboard prototyping space: