Hi Cosmo, I'm not sure what you're referring to. Are you referring to the gaps in your screenshot? Because they are not there if you unhide Structures.
https://i.gyazo.com/89d2c779aae51acc55d2b8c2a2d2dd38.png

Stage 2 and onwards have this ugly mismatch flooring. https://imgur.com/a/uTjAviY

Yes, I have included a "Hidden" crate filled with toolboxes. Since there is no official supported way currently, then the easiest way is to use that crate.

1) Find the crate, use the screenshot on Stage 1 to see its location (its above the middle shelf in the ballast room).
2) Take the toolboxes from the crate and put them into a cabinet.
3) Fill the toolboxes with everything you want to take to the next sub.
4) Put the toolboxes back into the original crate. Put on your diving suit
5) Switch subs and unload everything to the new one.
6) Return empty toolboxes to the crate and put it away.

This is much easier if you've got a few people helping you, and in my experience only takes a few minutes to load and unload everything. Also, this makes it so you shouldn't need to switch between the Stages multiple times to get everything as long as you've got a couple people with you that can help carry additional crates / ammo boxes / etc.

Is there a simple way to transport submarine inventories that I am missing?

Hi, Ghostwish. This sub is not intended as the starting sub in my series. You are supposed to begin the game with the Stage 1 sub and then move all of your stuff over from the Stage 1 to Stage 2 once you can afford it, and then from Stage 2 to Stage 3, etc. If you read the description I have included a crate that will assist you with this.

It's fine if that's not how you want to play the game, however. Just open up any of my subs in the ship editor and add whatever items you want and use that instead. If you have any questions just let me know.

Allright, problems with this guy so far: The sub starts off completely empty. Also? Can't order anyone to man the gun. Like that little diagram of the sub with the weapon systems doesn't show up. Other than that, once I bought some supplies, there was no problem.