What's the difference between creating a 'Content' or a new 'Pages>>Add Custom Page'?
Structure -> Pages menu link comes from ctools and it allows you to create more complex pages than your basic drupal core ones (Content -> Add Content link). This may include components comming from other modules (Panels, Fieldable Panel Panes, Views Content Panes and many other that intergrate with Ctools).

With Page Manager (and panels in general) you can create more complex versions of a page (or more, if you use the right contexts).