It is generally recommended to keep a flat structure when planning your website presence. That does not mean however you need to throw everything in the root directory for best results. You should not either however go more than 2-3 levels deep in your directory structure.
Below is an example of a flat structure:
| Flat Structure | ||||||||||||||||
| | ||||||||||||||||
| Directory (Theme1) | Directory (Theme2) | Directory (Theme3) | ||||||||||||||
| Page 1 | Page 2 | Page 3 | Page 1 | Page 2 | Page 3 | Page 1 | Page 2 | Page 3 | ||||||||
The actual web address (URL) for page three on theme three would look like:
http://www.yourdomain.com/theme3/page3.htm
