@"What you can do", if I understand correctly, you previously used "fpc.cfg" to add paths to your units, but it doesn't work in the new version of Lazarus? It should work as before, and shouldn't differ between versions.
How exactly did you install the new version? I suspect you have two compilers with different "fpc.cfg" files, and you're editing the wrong one. Make sure you only have one on your system.