You setup a variable before start as 0 and then update every few ms or whenever you click etc (up to you) in the range of 0 to 1 and apply that For 2D overlays: use 'ccbSetSceneNodeProperty" and property type 'Image Alpha' - ie something like:
ccbSetSceneNodeProperty(node, "Image Alpha", 0-1);
For 3D statiuc mesh use:
ccbSetTransparency3D(node, 0-1);
if you are already using 'Transparent Alpha' material you can also instead just adjust Param1 (0-1) also.