The Fan module is for your Facebook Fan Page, like
www.facebook.com/SourceCoast
The Fan module *only* works with URLs for Facebook.com Fan page URLs and does not work for individual pages on your website (including the home page). The benefits of the Fan module is that it can show the activity stream from your FB Page on your website as well as user faces who have liked your Page and some other things.
The Like button can work for any URL on your website. That can be your home page or each individual page. The Like count will be unique to *each* page on your site. There is no way to aggregate all of the Like's for individual pages on your site though, so you won't be able to say "We have 8,000 like's across 50 pages". So, many users will create a Like module that shows up in a sidebar or header area on all pages but has a URL for the home page. That way, all the Like's clicked on any page using that button will 'Like' your home page. You can still have other Like buttons on your site which are for individual pages as well. You can add those using the JFBCLike module, {JFBCLike} tag or with the JFBCContent plugin which can automatically add it to all articles.
Hope that explains, but if you have other questions, just let us know!
Thanks,
Alex