I tried to use Eclipse for Arduino development and I followed this tutorial too but it didn't work for me. Also I couldn't find normal description of how I have to use it. From the other side so called Arduino IDE in my opinion isn't IDE it's very primitive buggy editor(looks like amateur product).
To upload my program to Atmega controller I decided to use avrdude direct from the console, where I specify programmer type and hex file that I want to upload. In this case I write program in c and use avrgcc toolchain for compiling and linking. However the question about IDE is still opened for me(the main problem for me that I don't know how to debug my code without IDE).
Also exist Atmel IDE AVrStudio. I didn'y try to use it, my I will mention it like a variant that you can try if you want.