I recently created my first custom ship with the ship designer at the main menu. I noticed that you can select your custom civ fleet style, but the color scheme and ship appearance (pipes, hexes, etc) is not accessible. Here is the process I went through to get the ship uploaded for others to use with the right color scheme I planned for it.
1. I designed the ship in the ship designer from the main menu. It wouldn't let me use the color scheme i wanted so I just picked one. I saved it as a template, instead of a ship design.
2. I was then able to go to my custom civ, verify my new ship was in the proper fleet slot, and upload that civ update. I noticed in the screenshots of the custom civ, the color scheme I used in the ship designer was in the screenshots instead of the active color scheme on the custom civ.
3. I opened a previous save with access to the tech needed, but the design was not accessible.
4. I created a new game, teched up to be able to design the ship, and successfully uploaded it with the proper color scheme for the matching custom civ. Fortunately, it's just a freighter. So it didn't take very long. If it was a huge ship it this would have been a very long process.
5. Went back to the custom civ fleet page, updated the fleet with new color scheme made in game, and updated the custom civ.
Thank you for all your time and consideration. Loving the game.