You need a tool to convert the ACE files to another image file format, i.e. BMP. You can use Tgatool2 to do this.
[
Download link Tgatool2]
I suppose you know how to do the rest, but if not, here goes:
After installing Tgatool2, do File -> Load, then select the file you wich to edit (MSTS folder/TRAINS/trainset/[train]/[file name].ACE). After opening the file, press Export-> BMP, and select where you want to place the bmp file, which will be the file you'll edit. Edit the BMP file with a suitable program (MS Paint works fine), then open Tgatool2 again, open the BMP file, export it to ACE (not sure which one tho), replace your file with the original, or make a new file name, but that requires you to edit some other files aswell (those files defining which texture that should be used), but i don't know which these are.
Hope that helps.