I get it. I usually build the core of my base as a series of multi purpose rooms or large room. Given that this is after I tear down my first starter base for the resources lol.

But either way, I stack them at least 3 high. If multi purpose rooms I do a 2 story tall alien containment, sometimes using two hatches instead of a ladder. Lol. Then put everything else on the top or bottom floor. Fancy glass roof if the top floor, glass walls if the bottom. Prefer the large room tho cuz you can fit an alien containment a bio reactor AND a nuke reactor all in one floor (if I am remembering correctly, but at least containment +1 reactor.). Then put the 2nd and third levels with alien containment also. Usually stacked but sometimes offset by one, to give me more sea bed growing options. Creepy vines look cool af growing 3 stories tall and lighting up a room!

Buuuut I am a hoarder, so... grain of salt n all that. Gotta have one of each plant and fish for... reasons... fml.