To program an Arduino with Eclipse you just need to follow the Arduino manual for C\C++. As it says, you need to:

1. Install the AVR plugin. Which is just to add the repository: http://avr-eclipse.sourceforge.net/updatesite and install its software.
2. Create a C\C++ project type AVR Cross Project Application.
3. Code, build the project, activate the Release build configuration (which is the one that generates the .hex file), and upload to the Arduino (using the Upload project to target device AVR option).

Probably you will have some troubles when upload it. You should configure your the AVRDUDE tool for your device. For a Duemilanove in Linux a configuration (chosen project properties) that works is…

• AvrDude:
  • Programmer: Atmel STK500 Version 1.x firmware.
  • Override default port: /dev/ttyUSB0
  • Override default baurate: 57600
  • In advance tab: Disable device signature check.
• Target Hardware:
  • MCU Type: ATmega328P (which can easily be loaded from the MCU).
  • MCU clock frequency: 16000000

You just need to download the template and extract and import its two projects in your Eclipse workspace. Now you can use the arduino library.

• Arduino template for Eclipse

Blink:

#include <avr/io.h>
#include <util/delay.h>
 
int main (void) {
	long i;
	DDRB = 1 << 5;
	while (1) {
		PORTB = 1 << 5;
		_delay_ms(1000);
		PORTB = 0 << 5;
		_delay_ms(1000);
	}
}

Heartbeat:

#include <avr/io.h>
#include <util/delay.h>
 
int main (void) {
	DDRB = 1 << 5;
	while (1) {
		PORTB = 1 << 5; _delay_ms(250);
		PORTB = 0 << 5; _delay_ms(250);
		PORTB = 1 << 5; _delay_ms(250);
		PORTB = 0 << 5; _delay_ms(1000);
	}
}

• https://randoof.wordpress.com/2011/09/05/the-arduino-uno-or-duemilanove-from-one-to-the-other/ , Diferences between Duemilanove and Uno.

• The removable ATmega chip also means that when you complete a project and wish to use it, the chip can be removed and used in place alongside either a cheaper cloned version of the Arduino, or even make an Arduino yourself with the correct hardware, which is a lot cheaper than the Arduino and can be a lot smaller as well. For some idea of what can be achieved and for inspiration, have a look at this forum thread.

• A microprocessor generally does not have Ram, ROM and IO pins. It usually uses its pins as a bus to interface to peripherals such as RAM, ROM, Serial ports, Digital and Analog IO. It is expandable at the board level due to this.
• A microcontroller is 'all in one', the processor, ram, IO all on the one chip, as such you cannot (say) increase the amount of RAM available or the number of IO ports. The controlling bus is internal and not available to the board designer.