Using a CMS like WordPress, Joomla!, or Drupal for your web site is a good idea.  A primary function of any CMS is the separation of content and presentation (look & feel) from each other and from the underlying CMS application. To get the most benefit from your CMS it's important to understand that the CMS has constraints and standards that that allow it for function properly.  Following is a list of things to keep in mind when using a CMS.  My list is far from authoritative, so please make suggestions and comments.

• Do your information architecture before setting up your site.  Information architecture can simply be a good outline or site map.
  
• Understand thew conventions and organization of your CMS.  Yes, I mean read the documentation or the get book.  Joomla! for example does not have pages but rather has content items, menu items, and modules.  Once you understand how these work together you're in business.
• Keep design elements out of your content.  For example, only include images that are relevant to your content.
• Be careful with internal links.  Make sure that any internal links are constructed in such a way that your site can be easily moved.
• All styling should be done with basic HTML and CSS.
• Understand the key factors for good SEO with your chosen CMS. - http://website.grader.com/
  
• Content creators/owners should be responsible for maintaining their own content.  You should not depend on a designer or administrator to update content.
• Good design is important, but don't let design get in the way of your message.  There's more to good design than rounded corners or the latest JQuery menu effects.  - http://www.useit.com/