nat1 wrote:should I use the nxjc and nxj commands I have from the lejos nxj download?
No, Eclipse compiles the Java source code automatically as soon as you press save. Then when you want to run your code, you just use the regular green "play" button or use the Run menu. It will make you select the class that you want to run.
If you are using command prompt, just use javac.exe and java.exe to compile and run your iCommand programs.