Flatter side of the rim lines up with the non-drive side (the left side, non-cassette side, "other" side, etc). So sounds like your wheel is built correctly. If you think about the angle of the spokes, the spokes on the drive-side originate fom closer to the bike's centerline, and are usually more straight-vertical (and thus higher-tension) than the spokes on the non-drive-side. Moving the spoke-holes in the rim toward the non-drive-side evens out the angle and the spoke tension somewhat.