You can customize emblems with a variety of options. There are logos, letters, images, shapes, etc. that you can choose from. Combine them together and make a unique emblem. Obviously you can choose the colors of them as well as the background of the patch.
Under the Fleet tab, I think it's under permissions, change fleet emblem and you can see all the choices and options. Once you set it, you have to go to the ship/costume tailor and put it on your uniform and ship.