Regardless of what program you will be using, you basicly want to make sure for two things.
1: Once you are done with your design, make sure it has transparent background, and it should be saved as .png extension.
2. If your background is solid color (for any awkward reason), then make sure to crop your picture for only as much as needed for ship.

Thank you for helping me. I put it up as a work-in-progress, so that I can tweak it as nessesary. You were very helpful.

I don't think anyone is going to come back to this for an updated, but I figured I would cover all bases. I deleted my wireframe ship so that I could remake it. I couldn't go back and choose what Shadow Ops rank to put it under, so I had to delete it so that I could have the engine exaust.

I usually start with 220 x 220 as a base resolution, and then when I'm done, I scale the canvas down to the image size. You can also open up one of the default ship images and then wipe it clean.

In Paint.NET, if you use CTRL+C to copy a selection, and open a new image, it defaults to that selection size. An easy way to "resize" your image to cut off extra blank space.

I'll remember that. Thank you.