Yup. Unless you want them to glow or light up or something.
Though I'm somewhat unsure on where everything should be located on the model.
There's not a lot you can do except experiment. Each ship's texture is set up different, and without the converted model files you really can't change where the game looks for the texture at each spot (I.e. the UV map). Fortunately, in the developer.exe, the game will reload textures as you change them, allowing you to quickly change it without needing to exit the game.
If you really can't find something, you can try either a texture of colored blocks or a two way gradient to try and get some idea how the UV map is set up. Here's one I did when I was trouble shooting a minecraft texture pack, from left to right I did a black to white gradient, while from top to bottom I have a blue to red gradient, giving each pixel a unique color. If you have a pixel color tool you can even find the exact RGB values (might be a bit off due to shaders) and get the exact spot.
What's the plugin for paint.net? Looks easy there compared to some other things. Alpha channels has been my big prob so far and I hate Gimp (which is ironically the program I started in graphics on waaaay back)..
Well photoshop is certainly the easiest and probably most effective thing to use. If you need something free (like me), I've found paint.net is usually the fastest and simplest thing to use, I use it almost exclusively for UI work, or for just looking at CL textures like in this case. I've only just started using GIMP, however it seems better for more complicated things, like if you need to a lot of texture building, selection work, or for say the DA textures, where you need to modify each channel independent of each other (I have an extract channel plug-in for paint.net that allows you to get just one channel, but its a pain to get the R, G, B, and A channels as separate images/layers and then recombine them, so GIMP wins on that despite the annoying process to get the alpha read correctly).
Also its best to be able to do basic things in both, as having them increases your filter library, which can be a big help.