The JFBCSocial plugin is what we use to look for the {} tags on the page and replace with them with the correct Facebook calls. These are the { JFBCLike}, { JFBCComments}, etc tags and can either be put manually on a page (in the template, in an article, etc), inserted by one of our modules, or inserted by the JFBContent plugin.
The JFBContent plugin is used to automatically insert the Like and Comment boxes on content pages of your site. This is done by automatically inserting the {} tags for each into the articles, which is then replaced with the JFBCSocial plugin.
So, you should always have the JFBCSocial plugin enabled. You can choose whether you want the JFBContent plugin enabled.
The reason the likes differ unfortunately, is that we send a unique identifier to Facebook within the JFBContent plugin. We create this id based off the type of page you're displaying along with the id of the content.. so the identifier would be something like 'content_12' for article 12. The reason we generate this ID, instead of letting Facebook do it automatically, is because on many Joomla sites, you can reach the same page in numerous ways. For example:
index.php?option=content&view=article&id=12 (A page only showing article 12)
index.php?Itemid=27 (which would be a menu item to show article 12)
index.php?option=content&view=blog&catid=12 (A blog layout, each article could have it's own like box).
The last case is the most important, because when using the JFBContent plugin, we'll put like buttons on each article, but each like button would be unique to that article, not to the 'blog' page itself.
Hope that explains the function of the two plugins. You can use the Content plugin to insert the Like button at the top of the article, and the comments at the bottom and they should both line up. If you use the { JFBCLike} tag or module on the page though, you'll want to make sure you use the same id that the Content plugin is specifying (you can find it in the HTML).
We're working on streamlining some of the plugins for a future release to make it less confusing. Right now, we have a ton of ways to do similar things, and each one fits certain needs.
Hope this helps, but if you have any questions, let us know.
Thanks!