Arduino
I have just taken possession of one Arduino Uno R3.
This is the fancy Make: version so all components are SMD.
It has an ATmega328 as its main controller and an ATMega16 to talk to the USB port.
Here's its schematic. https://www.arduino.cc/en/uploads/Main/Arduino_Uno_Rev3-schematic.pdf
Arduino as development board
This board arrived at a convenient time for me, but what I really want to do with it is develop code that can be pushed into my Temperature Controller, which is based on the same ATmega328 controller. (Actually it came with the compatible ATmega8.)
Writing programs for Arduino
I know I can use the official Arduino IDE but I also want to know more about [Atmel Studio http://www.atmel.com/tools/atmelstudio.aspx]. Are there advantages for me to use one or the other since I intend to develop for both the Arduino and just plain Atmel AVR controllers.
It looks like Atmel Studio is Windows only? How can this be? How sad! Here are instructions to use it on Mac: http://www.thinkcreate.org/index.php/avr-studio-on-mac-os/ There is a toolchain supported for Linux, but no IDE: http://www.atmel.com/tools/ATMELAVRTOOLCHAINFORLINUX.aspx but I am more inclined to try Parallels with Windows 7 first.
Loading programs into Arduino
I am used to working directly with Microchip PIC controllers, programming them with a PicKit3. I find this to be very convenient. Using an ICSP programmer is also possible with Arduino.