The top - is your border - under this is shadow with reduced opacity - where i paint with black brush shadows on the ground (not always used) Under this there's layer for pasting your custom graphics (it could be your custom background, graphic for technology, building, unit etc).
The next layers are for units and promotions it contains backgrounds used by game.
So if you want use your plane with civ4 buttons style you can (i use this method) make screenshot of the unit in nifskope, cut the gray background, and select inly the unit (you should now how to work with selections in graphic programs). I just rescale selected airplane to the proper size (all graphics should fit the size of button wich is 64x64) and paste in the layer named "Paste Graphics Here". Here's the result:
If You have Gimp or Photoshop you don't have to worry about the alpha it contains alpha - so just export it as .dds.
If you don't have Gimp (freeware) or Photoshop but for example Paint Shop Pro or PaintDotNet (Note that for PaintDotNet you don't have .dds export plugin - so you have to convert it to .bmp) you should be available to open the files and export as .bmp. Don't forget in that situation to merge in DDS Converter with alpa (alpha chanel butons.bmp file)
Tested on Gimp 2.0 and Photoshop 8.0 CS, PaintDotNet 3.0 but i think it should work with older versions and other softwere wich could read .xcf or .psd files. It saved me a tone of hours and it's very useful thing - I hope it'll help you in creating buttons too.