Three greenhouses filled with fern can accomodate 30 personnel tops. But design is planned for 40. So go looking for palms or pines. Actually you need 3 pines at all. One tree for each greenhouse and wait as they plant themselves into other planters IF greenhouses are fully staffed.
So as I do - I fly with initial 10 heads and starting greenhouse filled with fern. In the meantime I get them to commander levels and research Helix and build rest two greenhouses. Find few pines. When battle against Helix is won, crew quarters move from lower level to top level, 3 commanders goes to work to one new greenhouse where I plant first pine. And let it spread and replant. When I have another 3 commanders ready to change jobs, I repeat the same with 3rd greenhouse. When two pine greenhouses outgrow the starting one with ferns, I delete the ferns and plant pine in there, along with 3 commanders.
Why commanders? Because they will never be moved from there, as trees will start to decay if no sufficient count of servicing personnel are working there.
And two turrets in each greenhouse - 1st by doors, 2nd - by slot where robot put plant in.

S - are Storage modules.

Well, 4 shields are not for looking cool. Unmanned they can keep you well and unharmed in green zone of spores or asteroids. Though for something more serious, like boarding parties or more harsh erm... space harms, you need put people in them. Best are commanders (put them there and do not move ever from there), because, again ship is designed to house 40 ppl, so put them to use :)
And even with fully manned shield modules I won't risk sit in critical zone of solar flares, longer than I can jump into system, run down to send harvester to grab a pine and run back to bridge to be ready to GTFO when harvester returns.
Next thing is defending when enemies get INside. Simple answer - turrets and barriers, and security gates... decontamination (questionable thing).
So starting from bottom to top, lowest level I call Resource level, where aliens can get in mostly and they have to not leave that level, ever. So in this for our service are turrets in tractor beam, deposit (in case you got different corporation with small deposits, then put turrets in corridors between deposits), refinery and underneath of these rooms. Also Energy barriers blocking all tunnels of Hangar and tractor beam, for easier containment, because disturbed aliens start to run around, personnel starts to chase them, nobody wants to work, the mess starts. Security gate is good thing if rest of the ship don't have defences yet, decon room too (once I found runaway mechanic crying outta fear in decon room when being showered with decon liquids; was grabbed with tractor beam, but the ppl overslept him and he ran out). Anyway these two - security gate and decon are more passive defences, helps as last resort if you have nothing more left or it's still early for massive turret production.
Then we get to storage floor, smallest floor, I just put turrets at every crossing and when they barge in, they drop dead instantly, leaving goodies on the floor for me to pick up after.
Next, bridge floor. With time you will have enough personnel to put one or two in every room there and they can defend just more than their workplace - corridors as well. But in early stages, just put turrets in corridors, best at doors into rooms, if boarders beam into room and tries to leave it, they will have to go past turret. Empty rooms w/o workers, like hyperdrive can have one turret, since they seem attack these sometimes too.
And finally the top level, the crew level, as I call it. 2 turrets per greenhouse, 1 turret per quarters and biotanks (and maybe reactors early). And like in floor before - in corridors - if they don't die in room, they die when they try to leave that room.
Tunnels of floors. Long corridors I arm with turrets, though not that many as before, when Helix is now contained with having quarters at bottom level, to avoid mass infection in long tunnels.

And robots. Put them on patrol at earliest. You never know, when you get fast spawning crawlers and they start knocking down your rooms like domino effect. Without fast repairs, you can loose critical sections of ship quite quickly. Robots can use beaming stations and turbolifts for traveling. I got beaming station near greenhouses, and one at bottom level, so bot carrying plants arrive very quickly now, I even can see it through window :)

And reinforcing. Truly, I'm not sure how this thing works. I tend to believe it takes more time to knock out the power node of reinforced module or it can burn longer w/o repairs until it is lost. But it's bugged at least for me, when I reinforce partially one module, others nearby shows they are reinforced too, but I need to turn building map 90 degrees few times, to see again, which modules are and which aren't reinforced yet and to what state. And it feels, like I'm reinforcing some modules again and again, or I forget them too quickly :D Anyway, seems kinda pain, and I hope it works.

This design is for Stahl Union III, which can be unlocked refining 60 Platinum in one round. Because only this corporation and Framen only can have deposit (48 capacity) and refinery this big. All other corporations has small deposits (8 capacity) and to achieve somewhat larger capacity you need add corridors and deposits down there, well, it's a bigger pain truly.
Ship houses 40 personnel, 200 storage capacity and 48 deposit capacity. Decontamination you are free select which one you like. I this time have variant A, in round before I had variant B, round before that I had no decontamination at all and only one octopus-type-crawling alien managed to run away, but was blocked by security gate. Turrets and barriers sitting in Tractor room must see, no one escapes through, so if you careful, you can remove security gate as well.
Tunnels of corridors of crew (lvl 3) and bridge (lvl 0) floors are patrolled by M10 Bots, which must ensure electric nodes are fine, in case of boarding of enemies or infestation of tunnels. Also put there turrets, so when you get down there to clean them, aliens will move and turrets do the killing for you. Also one more (3rd) M10 Bot patrols beneath Hangar, Deposit and Refinery.
Block tunnels with barriers turrets in Tractor room and Hangar, so anything trying to run and hide could be contained and killed. Also 4 turrets in corners sit in Deposit, about 2-3 in refinery, 4-5, in Hangar, covering each other killzones.

Before you found Helix, keep Crew quarters connected to Tractor room, and have M10 Bot ready, because they grow and pop out FAST. When you researched and healed from it, can move quarters to top floor where they belong in plan, other two diseases, won't do any harm to your equipment (at least not that FAST), you have plenty of time to go after sick personnel on their way to quarters and collect 10 sneezes for research.
Cr3-P robot can kick some tunnel crawlers, but it cannot make them hatch. I had one bot patrolling tunnels too and he attacked them only when they were moving. So you have to get in there yourself anyway, to disturb the nests, make beasts pop out and be killed in early placed turret crossfire and M10 (repair) Bot will see to repair any power node damage.
So my robot count is 3 cargo robots, preferred faster ones, 3 M10 Bots for repairs on patrols and 2 places for anything else, once I found big-ass military bot, I let him patrol long corridor in lvl 3, so he surprised boarding parties.

And this is how ship of this design look like when it starts it's journey. Should be called "Flying barebones" lol