Ye' old general discussion board. Basically, for everything that isn't covered elsewhere. Come here to shoot the breeze, shoot your mouth off, or whatever suits your fancy. This forum is not for asking programming related questions.
The files/folder will be in your workspace directory, which is a PITA I agree.
When you create a project, do not import.. that will copy everything into the workspace dir and not work from your web folder. Which is better for code control, but meh..
Because of an issue I had with Eclipse opening Zend Studio on every movement inside of Eclipse, I changed the project root folder to the web server root, then refreshed the file listing. Bing, I was in.
But strangely this does not sound like the problem you are having.