By drawing on two document Layers ( not Tool > Layers ) and disabling Render > Flatten you are able to use the Transparency modifiers of a material.
1 ) Fill the current document with the current texture, Texture > CropAndFill (CTRL+SHIFT + F).
2 ) Create a new layer with Layer > Create (note the newly created document layer is automatically selected).
3 ) Turn off Render > Flatten.
4 ) Draw your 3D tool on the canvas and enter edit mode.
5 ) Select a material with transparency modifiers and tweak those modifiers. The BasicMaterial and DarkEdge materials are well suited for this.
You might get some artifacting around the projected X axis of the displayed 3D tool but it should not be too distracting.
Hope that works for you.