The installer will surely add the scenery automatically on the scenery library.
However, if your scenery.cfg had a problem (like a syntax error or so), the installer won't touch it in order not to risk corrupting it even more, and also depending on some compatibility settings, it's possible your FS9 is not using the normal scenery.cfg.
These are some of the reasons why you had to add the scenery manually, but under normal conditions, the installer will do it automatically.