This guide cover the following parts of creating a ship for your species:

• creating the ship objects
  
• drawing the ship layouts
  
• creating the ship pet

The guide covers BYOS ships from FU a little (removing the background part) in the end of the second section of this guide.
The guide assumes you know modding basics (unpacking assets, creating objects).

These are any objects that are meant to be part of your ship by default, removable or not.
Usually, these include:

• Teleporter
  
• S.A.I.L. Console
  
• Fuel Hatch
  
• Navigation (Captain's Seat)
  
• Locker
  
• Locker T0
  
• Light
  
• Broken Teleporter
  
• Broken S.A.I.L. Console
  
• Broken Fuel Hatch
  
• Vertical Hatch (removable)
  
• Horisontal Hatch (removable, optional)
  
• Secondary Locker (removable, optional)

They are all usually located under this path:
For example:
If you don't know how to create according objects, you can use these as base.

Probably the most difficult part of the process is drawing 9 ship layouts, 9 ship backgrounds, 8 ship transparent layers with different levels of transparency, and editing 9 configs to go along with them, one for each tier of the ship.

You you don't want to go through this pain (at least for now), you can simply copy a vanilla ship, change the species name in the file names, and use it for your species.

Still, if you decided to do this, here we go.
Ship configurations are usually located under this path:
Here and below, <species should be the name of your species.
The files inside look like this:
Here, <tier> is a number from 0 to 8 inclusive (hence 9 tiers total).

Notice how T0 has less files than the rest. This is because it's using some files from T1.

What do we have here:
This step is simple but tedious:

• change the filenames mentioned in all .structure files to your species ones.
  
• update the blockKey.config file with your object IDs if needed.
  
• edit the png files. This is the hardest one in my opinion. Good luck.

If you feel like you've got the hang of it, fell free to make other edits as well!
If you're playing with FU and want to make your ship into a BYOS one, make sure that your <species>T0.structure file has the "backgroundOverlays" property as an empty list, like so:

This part consists of 2 steps:

• creating a ship pet
  
• adding it to your S.A.I.L.

If you'd like to use an already existing pet (a vanilla one or from another mod), you can skip the first step.
A ship pet is a "monster" just like all non-npc enemies (poptops, etc.), critters and bugs.
The difference is that its specific parameters make it:

• persistent
  
• ignore all damage
  
• have a bit of different lua logic
  
• use random sprite version out of a set of sprite versions

Most vanilla non-npc creatures in Starbound don't have these qualities.
Usually, ship pets are located under the following folder:
For example:
What's happening here:
You can create your own pet based on this information.
Now lets make it so your pet actually spawns in your ship.
All you need to do to make this work is to set the "shipPetType" value in your S.A.I.L. .object file to your pet "type", like so:
Or, if you're creating a patch for someone else's mod, then you should create a ".object.patch" file and put this in it:
My Enternia example: Alta Ship Pet - Snugget Patch[github.com]
That's it!

This is all I have to share on this topic. Let me know if there's anything I'm missing! ^^
The guide mentions patching in the 3rd section. If you're not familiar w/ it, here's a helpful guide:
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2124444255
More about ship upgrades:
https://starbounder.org/Ship_Upgrade

Testing upgrades:
https://starbounder.org/Ship_Upgrade#Admin_upgrade

Creating objects:
https://starbounder.org/Modding:JSON/Variables/Objects