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If you place them so their sides are touching you'll see a coloured border showing around them, that means you're getting an extra bonus. different groups of upgrades have different coloured borders and don't boost from each other.
You can stil have the upgrades anywhere in your inventory and they will give you their default boost, but if they're touching it will automatically give you an increase in power.
The maximum bonus available is based off the highest level upgrade, if you have the Theta or Omega upgrade, to get the highest boost you should place all the other upgrades on it's four sides in a cross shape, you can also benefit from 2x2 and 3x3 grids when you have a lot of upgrades which share a bonus, but always have the highest level upgrade touching the most other upgrades.
It's not always possible to configure things for maximum boost due to the way the game handles things but you can get pretty good bonuses.
Yes, I do wish we could move all the upgrades around, I don't know if some of them are bugs, but I've restarted the three modes many times and I always get the jetpack in a corner where I can't place any upgrades next to it, no matter how many slots I get in my suit I can't ever maximise my jetpack.
Most of your stuff will be aligned vertically for ship and both directions for suit, your multi-tool will be horizontally aligned due to the configuration of the slots.
If you can make or find a mod and have the blueprints unlocked for the base technologies then you can rearrange them as you see fit for maximum bonus.
Jetpack is always in the corner.
You can, if you wish, try and trigger the bug where swapping inventory in one of your base containers will cause a suit tech to move into one of your fighter slots. You'll be able to reconstruct the jetpack in whichever slot you choose, but wont be able to deconstruct the jetpack in your fighter slots, so you'll have to live with it or swap ships eventually.
http://steamcommunity.com/sharedfiles/filedetails/?id=824170423
I set it up this way to put the items that I commonly refuel in rows close to the top, and to keep the others in neat groups.
Obviously, I've used a tool to get the tech arranged like this, because the un-removeable items aren't in their standard locations. It's nice to be able to put the Jet Pack next to the Jet Pack Boosters!
In my case, I used the excellent raw JSON editor that's built into the NMS Save Game Editor (use version 1.1 --- version 1.2 JSON editor doesn't seem to save changes). Careful with that tool, it requires close attention to details.
Each upgrade requires its own slot. so you can`t stack them in the same way as some resources. (more than one to a slot).
But as has been mentioned, there is a upgrade performance/bonus system which is dependant on how you arrange them.
Life Support, 3,2,1
Breathing 3,2,1
Laser Multitool, level4 boosters, level3 boosters, level2 boosters, level1 boosters
Like that. Put the highest ones near the base tech, then the next highest until you get to the level 1 stuff. For the weapons, all boosters that affect the base tech will stack with other random ones from the same base tech so put the highest boosters near that one and go lower. eg. all laser weapon boosters can be placed next to other laser weapon boosters.