I normally don't work in Eclipse but I'v been asked to deliver some of my work as a eclipse project. And I'v started to working with it a bid.
After importing and setting up my make targets and debug settings everything working fine but Eclipse gives a "Symbol ... could not be resolved." every time I use a function from the SDL library. As I said everything is compiling and running fine, but is't really hard to find any errors in a file that has 40 or so "Symbol ... could not be resolved." flags.
I ran into this similar scenario with STL libraries when using the QT Plugin for Eclipse. Everything would compile just fine and produce a functional executable but the Eclipse editor would tag every line with STL functions as "Symbol ... could not be resolved". I was able to fix the problem by adding the proper include paths in to the project settings.
For a QT project it was Project->Properties->"C/C++ Include Paths and Symbols"->"Add External Include path...". The paths I added were:
C:\MinGW\lib\gcc\mingw32\4.4.0\include
C:\MinGW\lib\gcc\mingw32\4.4.0\include\c++
C:\MinGW\lib\gcc\mingw32\4.4.0\include\c++\backward
C:\MinGW\lib\gcc\mingw32\4.4.0\include\c++\mingw32
C:\MinGW\lib\gcc\mingw32\4.4.0\include-fixed
C:\MinGW\mingw32\include
Then I right clicked on the project and selected Index->Rebuild once the rebuild was complete all the "Symbol ... could not be resolved." disappeared from the Eclipse editor.
I found this to work for both Eclipse 3.6 Helios and 3.7 Indigo using CDT 7 or 8 with QT Plugin 1.6.1 and MinGW 4.4 for QT.
Although this fixes a slightly different issue, hopefully it steers you in the right direction.