Welcome to subsim,
zzaj19855 
The easiest way to learn how to make this mod is to look at one of the submarine skins that's been done already. Go to battleflags.net and download any of the boats in the submarine section. Then look at the textures in the ....\Data\Textures\TNormal\tex folder (the ones that end in T01 and T02). You will see what the conning tower skin looks like with the emblems on it. If you want to see how the killflags are done, go to battleflags.net in the killflags section and download the files in any one of the skippers folders (especially the zip files ending in _PSD). After extracting the PSD files, open them with Photoshop (or Paint.net) and you will see how the flags are added.
If you really want to make these flags and skins, we can give you the templates that we use for the flags. You'll need a good graphics editing program (We use Photoshop and Fireworks), though.
Hope that helps and feel free to ask any other questions you might have