I've used EEKeeper 1.01 and 1.02 fine with the Steam version of BGEE. In the settings screen, I set the installation directory to \Program Files (x86)\Steam\SteamApps\common\Baldur's Gate Enhanced Edition\. If I recall right, you must include the trailing backslash.
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I've used EEKeeper 1.01 and 1.02 fine with the Steam version of BGEE. In the settings screen, I set the installation directory to
HTH.