The best plan is to create all those subfolder as a part of the original design.
You can still go back in and organize things into those sub folders but when you do that, any relative links on that page will need to be changes, that includes the navigation menu, images, etc. And since the URLs will have changed, the new, rebuilt site will need to be reindexed in it's new configuration.
Think of changing the folder structure as a major site rebuild... certainly possible and often something many sites go thru. Just realize that this is a major rebuilt and all links will have to be checked and edited as needed.
Sub folders based on what type of pages you are using is good for an intermediate solution. Once you start getting higher amounts of pages, you'll want to make them as dynamically generated as possible. Case in point, read in the URL with variables and determine how to format the page. You can use modrewrite to make the URLs user friendly. If you aren't using some sort of server side scripting for things like includes, you really should.
I would not recommend using a folder for each page. The physical structure should follow the logical structure. Oh, and bear in mind that changing the structure and file names can play havoc with your ratings! You may need to use redirects to keep the old url's working, at least for a while.