Transparency of Alpha Texture?

Let’s say we have a material with Alpha=0.
Also we have a PNG texture with alpha channel assigned to a slot 1, set to affect Col and Alpha. Now we have a material which is transparent in respect to alpha channel of that PNG texture.

The question is: How now do I affect Alpha of that material? If I assign another texture to a slot 2 and set it to affect Alpha, it does not influence areas that are opaque in PNG texture, however it does affect areas which are transparent in PNG (so I can make previously transparent areas less transparent, but not vise versa).

Try to play with blending method ( Add, Multiply, Subdivide etc.) and/or inverting influence.
And sometimes better idea is to have separate textures for Col and Alpha.
I think it should be posted in Texturing section.

Did you hit the ZTrans button?