After I checked out one of those projects, I used the Export as MyEclipse Web Project.
I then realized I misplaced the Webroot folder, that means I had to copy web.xml and other files from the original project folder into the MyEclipse one.
I have not found any option or settings page to change the Webroot folder! My quick (and dirty!) solution has been to delete and checkout again the project setting the right Webroot folder, but I believe there must be another way to perform this task!
Giovanni, Great question. If you go to your project properties and open MyEclipse > Web, you should see your Web Root directory listed there. You *should* be able to edit it here in a future release, but for the time being you can edit the .mymetadata file in the root of the project directly and change the value there.
NOTE: You will have to be in the navigator view to see that hidden resource to edit it.