Your programs will need to be turned in using turnin on the CS department system. Your programs must compile without error using javac.
You may do your programming however you wish, but I have suggest that you use one of the following methods:
Good editors include emacs (either GNU emacs or XEmacs on Windows and Linux; Aquamacs Emacs is my favorite on Mac OS X) and JEdit. Stupid editors that are not helping you as much as you should be helped include Notepad and vi. You will save lots of time over just this one course, much less over the CS major, if you switch to a good editor.
Warning: if you use other tools, you must be sure that they don't do strange things with your code (e.g., add package statements, or rely on custom libraries that are not part of the standard Java API) that will cause it not to compile at the command line on a Linux system.