In general, IDEs have some kind of a dialog box that lets you specify information about how to run your program. The dialog will let you set command-line arguments along with JVM arguments, environment variables, etc.
I went and Googled this "NaviCoder" -- thanks for the laugh, by the way, more on this later -- and it looks like this "Setting Run Profile Command" panel may let you add arguments, although I can't tell for sure:
http://www.navicoder.com/manual/online_manual/ide/java/RunProComApp.html
Anyway, despite that website's claim that NaviCoder is powerful and popular and wonderful, I've never heard of it, and the online manual makes it look positively dreadful. There are many better choices available -- don't torture yourself trying to make this toy IDE work if it's preventing you from doing something as simple as adding command-line arguments to a program. Eclipse, NetBeans, or for beginners, BlueJ (all these are easily Google-able) are industry standards and are all fine pieces of software.