You could try using trans white on the matte with the brown layer beneath it then use a blend mode on the brown layer over the blue one. Some of the new blending modes might include an alpha stencil or luma stensil. If you don't have any success try premultiplying the matte into and RGB .mov and using it as a standard black and white movie and do the same as decribed above.

The only surefired way I can do this is in Shake, AE or Combustion right now as a trackmatte or using a luma or alpha matte.

Again, It is very much needed in logo and live compositing where you composite a logo over either another layer or a live input. The only way you can make everything transparent around the logo, unless it is pure black and/or white is to use a matte, Richard.

Richard this is much like trans black/white except we would need it for any range or combination of colors. You can achieve this in Quartz.

Christian Choi