Structuring stuff has also another very bad disadvantage for me: folders and files which are "out of sight" become more like hiding places. I need to have everything thrown up in my face at the press of a key to really use it.
Just to address this one issue. If you structure things the way that Mark suggested, then dragging the root directory to the TextMate icon will create a project, and you can visually inspect the contents of the project (the files and folders) in the drawer. If it is not open press control-option-command-D to toggle the drawer.
All the best, Mark