I don't have all the background information on this because it was a year or so ago when I set up our RTC project area and it was the first time, so probably I didn't know enough about what I was doing.  I created one component, CCM, and when I loaded our initial code, it ended up in the directory structure CCM/src/...  The .project file is in the CCM directory.  When we moved from our old source code control system to RTC, the CCM directory was not in the path and this caused some minor build problems which is why I assumed that having the CCM directory was "just one of those things" about how RTC behaved.

I ran across another RTC project area today which has two components, say CompA and CompB, but the component names are not the top-level directory in the file structure.  The owner of this project area told me "when I create a new Eclipse project for a new bundle and go to check it in, I do "right click->Team->Share" and then the wizard asks me which of those components to put it in".  This project area has many projects, but they are in directories named, say ProjectA, ProjectB, ProjectC.  In my project area, it would be, for example, CompA/ProjectA, CompA/ProjectB, CompB/ProjectC.

So apparently you can build project areas in which the component name is part of the source tree path or not. Having the CCM directory works well for us, as it is an excellent place for scripts to build the whole project.  This creates exactly this problem for the new project I found as they have not dealt with a full project build yet and have no common place to store any build script for the entire project.  Is there a best practice here? 

If it is significant, our initial CCM project was created until RTC 3.  I'm not sure of the other project, but both are now on an RTC 4.0.1 server.

Chris