Submitting paper to IEEE journal using the standard `article`/`proc` LaTeX class
I disagree with Bill Barth's answer: I strongly believe that you should use the LaTeX classes that IEEE has provided you with.  The reasons are two-fold:


The reviewers will be used to almost always seeing IEEE submissions in IEEE standard formats.  If you submit in another format, it will likely prejudice the reviewers against you, as it will appear "amateurish."  Whether or not this is fair, it is a risk you are taking with your paper that there is no need to take.
Many IEEE journals have length constraints, and some are quite adamant about them.  If you submit in a non-standard format, it will be difficult to tell whether you are actually complying with the length constraints or not.  This may annoy the editor, again unnecessarily.


IEEE formats are pretty easy to use, and have really good instructions.  Since that is the case, I simply see no up-side to avoiding the standard formatting, and plenty of down-side.