Currently if you create a folder in the TestComplete IDE, it does not create a folder in windows. I believe that it should as when I went into my project via Windows Explorer, I opened up my ProjectS...
You can still do this by manually creating your folders and files and adding them in. Having this be done all the time would not make sense for the reasons I mentioned above.
Also, having to files / classes etc... named the same thing is very bad practice.