It's so:

When you have chosen a project in the "all projects" window you will be able to add files to it. When you have chosen a file which you want to add, the software evaluates the file type and sets the subfolder as follows:

file type subfolder
-------------------------------------
index.htm; /
index.html

*.htm; *.html /html

*.doc; *.txt; /doc
*.rtf

*.gif; *.jpg; *.jpe; /pics
*.jpeg; *.png;...

*.css /styles

*.js /scripts

-------------------------------------

Though you're able to change the subfolder. Beside this I'm working on an ability to set a project folder and the opportunity to copy each file to this folder when you're adding the file to the project.

Is this the "directory structure" you've meant?