Just not getting permalinks

I have a hard time understanding the instructional articles. I do have a new version of WP and went in to enable permalinks. I used the suggested tokens and it wrote successfully to my .htaccess file (mod rewrite is on). But WP itself still calls everything using the “?” method. Am I now supposed to go into all the function files and change how it calls things?

Also, are WP blogs (out of the box) supposed to have a list of recent posts in the sidebar? I have archives and categories, but no recent posts.