Solved! Go to Solution.
Lefteris,
That is controlled in the main config.xml in the map component just change the top="40" attribute to your new height of the header controller.
<map wraparound180="true" initialextent="-14083000 3139000 -10879000 5458000" fullextent="-20000000 -20000000 20000000 20000000" top="85">