The deeper in the neck you place the rod, the better it works, until you put it too deep... (I've done it too, early on
). About 3 mm (1/8") of wood under the rod is pretty safe, and seems to be a good compromise. The higher up (closer to the neck's "natural axis") you put it, the harder it has to work, it gets harder to turn the nut etc. BTW, because of the geometry of the cross section of a common neck profile, the natural axis is close to the fingerboard / neck shaft glue line, or so I've been told.