First make sure you're using PNGs for your clip map, or at the very least 100% quality JPGs. Highly compressed JPGs dirty your blacks and whites and make any blending messy.
This map must be a black-and-white image. Indigo doesn't support alpha layers in images.
In Blender, go into a different layer from your scene layer and create one plane. Assign this plane with a new material called OPAQUE. The plane won't be rendered since it's in a different layer but will act as a placeholder object for your material so that it doesn't get deleted upon saving.
Now return to your render layer and select the mesh where you want the alpha material applied. Assign this with a material called LEAVES.
Now go into Blendigo, select this mat and assign it a BLENDED material type. Load your B&W alpha clip map in the texture field, this will be used to control the blending between material A and B.
The black areas of the map will let the material on the left show through while the lighter part will favour the material on the right. So assuming the leaves correspond to the dark parts of your clip map, select material OPAQUE as the first blend mat on the left and NULL as the mat on the right. This should make any object mapped to the white of the clip map disappear.
Sorry but you did say as though you were a five-year old...
