If you want to add more logos you have to convert the PlayerTheme[...].windows and the PlayerThemesDef into txt, I think in these files are the positions for logos.
But, if you want to replace an existing logo, that is much more easier. Just make a copy of RaceLogos.tga (it's in the Textures folder) and open it with photoshop or with gimp.
As you said you're familiar with 2D, so just delete an existing one, and draw your new logo. You can play with fading (as the originals are also fading from dark trough bright to dark.)
As you can see, there is an alpha channel. You have to make the alpha for your logo and place it properly. The funny thing is that there are other 3 sizes for the logos, you have to raplace them, too.
If you're ready with the logos, just make a new mod for it or place it in an existing mod, (in Textures folder) and when you apply the mod, your new logo will be in the game.