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Hey, Dave from the Help Team here! Its really up to you how you want to structure your campaigns and by no means would be doing something wrong if you had multiple campaigns for different areas of your website.  This is a common practice for Moz Pro users who want to have separate reporting.  My recommendation would be to at least use one campaign slot to track the entire site, then use the other ones to have your more targeted campaign reports.  Hopefully that helps!