the spoilers are for mechanics and modules refereed to as buildings in this guide
the picture is an early build but the basic idea is the greenhouse is in the center.

-bridge on the far front (bow) with reactors. these are the most valuable structures, so they are kept away from where the enemies spawn.

-the rear (stern) of the ship is for the hanger, tractor beam, storage, refinery and depot. these areas are the most likely places to spawn enemies.
its true that the green houses can also spawn enemies when installing a plant but that can mitigated by being present or putting security cameras/turrets in the greenhouses (which is also a good idea if you're expecting pirates)

-the left (port) side of the ship is where i place research, workshop, alien lab, clone lab, respawn chamber (connected to cloning lab).

-the right (starboard) i put crew quarters, recreational buildings (like the bar) biotanks and one spot for a turbo lift

the left and right are interchangeable, the idea is to have research together so there's less travel distance in between missions to planets/alien stowaways. the other side you can basically forget about after you place them, crew quarts is really only under threat when pirates are involved.
3 of the 4 sections get a turbolift and beaming station. invaders and aliens can use these to zip around your ship so if you have a beaming station its best to keep it on the other side of a security gate or decontamination room (both benefit from the use of shields and turrets placed above and below to halt invaders)
i've had humanoids spawn in the tractor beam room and run to the bridge, after that happened once i put shield up at the door and turrets behind it to stop that from happening again.

for late game i attach hyperdrives and shields to the front near the reactors on the 3rd floor up reachable with a turbo lift sometimes beaming stations
for extra greenhouses (up to 3) they are attached to the right above the crew quarters these always have one beaming station
the ship assault can be places anywhere but i tend to put it with the research buildings because the respawn room is close.

this is my first guide (im sure you can tell haha) so if you have any input i will take it into account for potential edits and future guides.