How should I fix the problem of duplicate content created by my CMS system's manual page alias feature?

duplicate content by itself is not 'bad for SEO' (unless it's done on purpose to manipulate search engines). It has a slight effect in that the SE may decide to crawl, say, 1MB from your site today, and duplicate files will mean that less of your site gets crawled. The other effect is that, when the search engine decides that your page shows as a result of a search, how does it know which of the two pages to show? (this is where the 'canonical' link acts. It tells the search engine "use this page", otherwise the search engine will pick one of them at random which may not be your preferred URL to show)