Theres a "subtract" shader that comes with MMF2 HWA.
What you need to do is change your object from using an "ink effect" to using an "effect" (pixel shader).
In the level editor, under the properties tab of the active object, you'll see a field called "effect". Change this to "subtract", which is under the "Standard" group. Theres no parameters for this effect, but you can adjust the transparency (same as alpha channel) by adjusting the "blend coefficient".