Ok, so if you search Google for "TGATool 2A" then that is what opens the .ace train pictures. And on UKTrainsim, go and find Route Riter. That comes with aceit which is a tool to send edited .bmp/tga pictures and transform them into .ace files, which are the pictures that MSTS loads for a train.
When in TGATool, open whichever .ace file you wish to edit, and then click "Send to editor", it will open it in MSPaint for you. Then save it into BMP format when you've finished, and open it with TGATool. Then you can export it into an ace file which can be read by MSTS.
That's how to edit your trains. (But if you create something you wish to upload, then do ask the permission of the original creator first!)
If you wish to have transparant windows, then you'll need alpha channels. I'll explain how you do those later if you don't know how.
Harry
P.S: MSTS models look much more realistic in 1024x1024 textures. I'll also explain how to do those later, unless somebody else wishes to save me the bother...