You have a container depot.
https://gtm.steamproxy.vip/sharedfiles/filedetails/?id=2568792526

The containers are brought in and placed in bays so they contribute their contents to the base. You place a container in a specific spot marked out for incoming containers. For example, where the container is in the top right, away from the bays.

The challenge is this:
Create an automated system that allows you to pick up the new container and have it placed in a specific bay.

We don't have sensors to detect if there is a container already in a bay, so using logic is not possible. Therefore we would need to tell it which bay it needs to put the container, possibly using switching connector blocks.

The limitations are that you cannot drive a vehicle or use a cockpit, the system must be fully automated once it has been told which bay to put it in.

Remember that the container may require to be rotated as well, the container on the top right of this picture is facing the wrong way.

It will be acceptable to use switching connectors in a sequence to control it. We have powered rotors and hinges, so adding power to something to make it do a task, such as rotating the container, may be required.

Credits: Thanks to BCP for his Bumblebee Loader which I use to collect these containers, along with the idea to create a mobile container depot.

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On a side note: I requested several time for logic to be added to the game, which would have made tasks like this able to be fully automated, but now Craneballs has pretty much abandoned the game, that will never be added.

I really wish they would open it to modding so modders can add things like that. I would love to have automated system for the base, including one way conveyors to ensure nothing uses the machines inventory, (I hate when the mining rig fills the constructors inventories and leave no space for the stuff that gets made), also units that empty a mobile container completely into the main storage so that it is empty and ready to go back out again instead of having to do it manually.