Can not agree with this more. The student edition of EndNote is available for $120, about half the standard price. In addition, to formatting your reference list, you can also attach the article to the EndNote entry for easy location and retrieval. And, if you use the cite while your write tool reformatting is as easy as selecting the new style and updating your document. While you might not think this important now, if you submit your manuscript for publication in another style (e.g., APA to AMA), this conversion occurs almost instantly when you apply the new template.
As for formatting the actual MS Word document, it is not that difficult to create a template with the appropriate margins, font, and headings.