The following screenshot is an example of folders organized into categories in the thread pane:
For comparison, the original layout of the Blogs account is as follows:
Notice how the server can be categorized as one thing but some subfolders can have a different category from their parents.
Setting up categories is easy. You just right-click on the folder name:
After that, you can select a current category or type your own in:
As you can see in the background of the last picture, even in categorized mode, the servers will still highlight if there are new messages, like normal.