In the map js file, find the line that creates the map control and change it to the 3D control.
depending on how you define the map control in the wizard, the line will be slightly different, for example, if I select a small map control in the wizard it will look like:
map.addControl(new GSmallMapControl());
to change this to use the 3d control:
map.addControl(new GSmallZoomControl3D());
The following page lists all of the possible values:
controls.html