The windows for all the cars in GSC2012 (so this includes the Mini) require a little extra work to have correct transparency, as the template and game have no way of magically knowing what you intend to be transparent. As such, you need to create two textures - the "diffuse" texture which will be used for your colours, and an "alpha layer" texture which will control the transparency.
Here's what looks to be a decent alpha layer tutorial for photoshop:
http://www.axialis.com/tutorials/tutorial-misc001.html
The idea is you put your number on the >LOGOS HERE layer, without unhiding any layers. So that you have something like this:
Now make a flattened copy of this, so you have a second texture to work with. We'll refer to this as A.
Go back to the PSD, then duplicate this layer and move it above the "alpha_FANAVID" layer in the stack. Then unhide all the "alpha_" prefixed layers. It should now look like this:
Again, make a flattened copy of this (B). You should now have A, B and the original PSD.
Now refer to the tutorial I linked to before (or another if that one's a bit baffling, I didn't read it through) and make B the "alpha layer" of A. Then save that file as a DXT5 dds, with whatever naming is appropriate.
This isn't the most efficient workflow but is the easiest way to explain it
(The car livery templates themselves are slightly different in that they don't use transparency at all, the alpha layers there control reflectivity and as such a generic one can be built into the template. Clearly this wouldn't work for windows, where the numbers are unique to each car and as such require a unique alpha layer created for them)
