If you take a look at the structure of the Eclipse Platform Runtime Binary archive and the Eclipse GEF archive, you'll find that both have an eclipse root folder which in turn contains a features and a plugins folder (plus some other files and folders).
When extracting the 2 archives they should be merged.In other words, extract one, creating an eclipse folder on your drive (on windows it could be for instance C:\eclipse, which should contain C:\eclipse\features etc.). Then extract the other making sure, the archive's eclipse folder goes into C:\eclipse, which in turn would mean eclipse/features goes into C:\eclipse\features, etc.
To verify that you've verged them correctly, check eclipse/features which should contain both an org.eclipse.platform_[version] folder and a org.eclipse.gef_[version] folder ([version] would be a very long version string.
If you still don't understand, you're welcome to post a directory listing here.
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