DEsh,
If you install the Nios Embedded Design Suite, you get Nios II Software Build Tools (SBT) for Eclipse. Open it and select File -> New -> Nios II Application and BSP from Template. From there you can either run web server or simple socket server and it creates the project.
I've only run the web server demo and if I remember correctly, the only change you will have to make is to the values that are normally stored in non-volatile memory like IP address and mac address. I hard coded them to make it simple.
The configuration device on the BeMicro SDK already contains a configuration with the whole qsys system including a working DDR and Ethernet interface. Once you get the project compiled, you should be able to run it on that board directly. You'll need the sopcinfo file which should have come with the reset of the BeMicro SDK materials. You can't edit that file in Qsys but you can open it in a text editor to get an idea of what's in there.
Good luck,
Scott