I assume you installed the CDT plugin for Eclipse? What is your OS, and what compiler are you using? Have you verified that your project is using the correct compiler, etc? Eclipse is picking about that sort of stuff.
Also, for me, on Linux/Unix systems at least, I MUCH prefer a simple Makefile and the standard C compiler options. If you are using Visual Stupido on Windoze, then you should really use the VS environment.