Eclipse may or may not be pulling the paths to index from your build setup, depending on the configuration. Most likely, it is not…it’s building correctly because your build setup is just fine, and you can probably build by hand.
The CDT indexer (which is the engine for deciding where all those pretty underlines, as well as code completion, F3 declaration jumping, etc comes from) isn’t smart enough in a lot of cases to parse out your Makefiles and know where to look for headers and source. You need to tell Eclipse that information manually.
Go to Project Properties -> C/C++ General -> Paths and Symbols.
The amount of work you need to put into this can vary greatly, depending on your environment. For me, it was only necessary to add scratch and src as library paths. If this external library is the only thing giving you headaches, then you probably just need to add the paths for that library and reindex:
Right-click on the project and select Index -> Rebuild