Rolio is designed so the lightning connector sits flush with the top of the Rolio in normal application. However, it is possible to position it in there slightly raised from the surface and still coil the cord. The coiled cord will lock the connector so it will not get pushed down when you place the iPhone to charge.
We recommending raising the connector to the same height as your case's thickness so Rolio can support the device's weight when it is docked.
Please note that this method may not work for very thick cases (over 5mm / 0.2").