How to structure theme folder to make it more manageable?
I typically put all TPL's in a templates folder, further subdivided by categories such as views, node, page, etc.

Here's an example folder structure from one of my recent projects:


themename 
- fonts
- images
- scripts
- styles
- templates
-- node
-- page
-- user
-- views


Basically, the only thing that goes into the root folder is the .info file, and the template.php file. Everything else is subdivided by category.