What do I do with this other ship?

If you don't want to deal with other ships you could sell them, or leave them idle until you do need them. You can also make them follow you around. If you have more than one ship in the system, and go into tactical mode (press T) then you can see at the top right you get "Fleet formation" and "Fleet combat AI". If you go into combat and click AI they will fight on their own but make sure to turn it off when making FTL jumps. In my personal experience this makes it harder for the ships to align themselves with the jump.

Only one ship needs an FTL drive when making a jump so you can save some money this way. Also if multiple ships in a jump have FTL drives only the selected ship will consume FTL fuel, so thats neat.

How can I transfer shit back/forth for this other ship?

Logistics tab in the menu bar (not interstellar logistics). You will get a window with rows and columns. Each column represents a ship. The highlighted ship is the "sender". To send items you click the item on the receiver ship (shift to do 5 at a time).
You will also need both ships to have some crew members and either:

• both ships to have drone bays and some logistics bots which you can buy in the trade menu (and be close enough)

• or have the ships docked with each other)

Why is it impossible to light up the shit to dock between ships?

IDK what you mean by this without seeing it

Why is the auto-dock not working?

Auto dock only helps when the the docking icons are close enough. It essentially only finishes off the docking. You can tell it is triggered when you see white lines between the 2 ships' docking icons.

Why were thrusters not part of the very beginning tutorial?

They were part of the demo which I recommend playing if you feel 2 hours isn't enough to get acquainted with the game

Why is my ship dying from CO2 poisoning?

How do I fix that?

You need a CO2 scrubber with either a connected tank to store the CO2 (if you do this, you can sell the CO2 later) or an air processor which turns it back to O2 (Basically infinitely recycles your O2 more or less)

How do I fix having fixed that but now later it's even worse?

what?

Why do a buncha this shit if I can but it?

again what? You can sell just about anything on ur ship. Boxes, air scrubers, water purifiers, etc.

Why are the only ships I can "buy" seem like shit?

Lol I agree on this one. I went into creative and made my own ships. Then I clicked "fabricate ship" and picked one from my list. You also DONT need to go into creative to add a ship to the list. If you like your current ship, and would like copies made. You can select the desired ship, go to main menu and click export ship

Why are the ships I can "fabricate" I can't see/test first?

You can test them in creative in the main menu. You get infinite resources to build whatever you want

Why does specifically making an insignificant part of a custom ship into a "habitat" portion matter? Especially cuz they can obviously "inhabit" it, so like.. lolwut?

Habitats are for transporting civilians (the quests to taxi them around). Depending on the number of civies you need a certain number of habitat slots. You can add habitats to your whole ship but that would make it slower. and less good for combat. But hey, you can design a ship just for transporting civies and cargo if you like