My models need a model file in .x accompanied by D, N and S texture files in .dds format, how would i make my model opaque? For the game engine I am working with I need to have my models in a specific format.

They need to have:


.X format model file 
.dds format Diffuse texture
.dds format Normal texture
.dds format Specular texture


These textures need to be baked with ambulant occlusion.

Now I know how to model a standard solid model, unwrap it, bake it and export the AO and UV's via the UV image editor, then export the model as .x (i have the plugin). 

At which point I use GIMP to merge them, add the textures, and use filter to create D, N and S images, then convert them to .dds.

That all works fine.

But how do I, maintaining the same file structure, make part or all of my object transparent/opaque, for example if I was making a wine bottle?

If anyone has an answer, simple step by step terms please, I get very confused very quickly :P
OK, I've managed to answer this myself. I was messing with blender last night, trying some other stuff when I stumbled across the answer myself. 

You don't actually need to set any alphas in blender (except to tick the alpha box when you hit new image for the UV unwrap), it's all in the editing of the textures afterwards.

For GIMP users, simply edit your UV textures as you would normally except this time right click on the texture layer you want to be opaque, select mask layer and chose white (full opaque). 

Your texture should now be opaque, to choose how opaque it make sure the texture layer is selected and use the alpha slider located between the blend drop down and the layer list (before you do all this make sure the image you are using is in a format that can have an alpha channel, like png etc).

If you want to give it a coloured tint, or maybe darken the opaque image then use the fill tool on the mask to apply a colour. 

Then just finish up the textures as you would normally, it should now be transparent in the areas you chose.