Right now I have pages like "about", "resources", etc and the urls are /about and /resources with a custom permalink structure as /%postname%. For "news" section it's the posts and it's at /news and that's great. The problem is I want the new stories to be /news/the-name-of-the-story not /the-name-of-the-story. Can that be accomplished in the wp admin area? Or is that a custom .htaccess trick? Also, news is in categories and /category/category-name lists the posts in that category and the story for those should be at /category/category-name/the-name-of-the-story. Is this even possible?
The custom permalink field on the settings->permalink screen only applies to Posts. Not to Pages.
WordPress Pages always live at the "top" of the URL tree. /about /whatever /etc. Posts live wherever the custom permalink string defines them to be.
So, in your case, your permalinks custom structure would be "/news/%postname%/" and would not affect your Pages permalinks of "/about" and "/resources".
For instance, to put all Posts under the sub-directory "/blog", your permalinks custom structure would be "/blog/%postname%/".