I personally have used Eclipse CDT before, but only in makefile mode i.e. to build anything I'd manually run the makefile. Basically I used Eclipse as a glorified editor. Here's how I worked things:
Everything part of the otherall solution came under the same workspace. Each library/binary was its own directory and project, so that I could make
each as required. I also had a separate folder (project) for tests with a makefile that built all the test exes I wanted to run so I could do valgrinds on simple bits of it.
As I said, I used make and not Eclipse CDT's built-in building routines - to that end I'd say it really doesn't matter how you structure it - do whatever makes sense / conforms best to the UNIX principles.