Clones can be cultivated in the Cultivation Hall. To be able to do this, you need research the Clone Cultivation I in the Tech Hall. That particular technology requires to have fully repaired the 3 Energy Halls. This will both unlock the production of Clones and the ability to use them in the Sky.
Upon unlocking clones, a new clone button appears in the Sky interface. There, you can add up to 8 clones in the Clones Sky Team (CST). You can also freely activate and deactivate the use of clones in Sky Combat through that interface. You can also destroy your assigned clones but you cannot remove them from the team without killing them.
During Sky Combat, the clones in the team can get damaged if you win the fight but your Airship leaves battle damaged:
Lower: May suffer damage, if Remaining Energy < 75%
Higher: May suffer damage, if Remaining Energy < 50%
Super: May suffer damage, if Remaining Energy < 25%
You do not lose clones if you lose the fight. If you lose some clones in a fight, you'll be informed of the lost clones in a screen and you can choose to forfeit the win in exchange for their safe return. If you suffer losses and accept them, you'll recover part of the clones creation cost in the loot as well as a small accelerator.
The Clones Sky Team (CST) size is limited to 8 and it is currently not possible to increase it. In that team, you are limited to 1 Super Clone initially. It is later possible through research to increase the number of Super Clones usable in the team.
To be clear, the CST is never used alone, it supplements your regular teams without counting towards leadership.
During combat animation, the clones are displayed on an upper deck if the CST is activated.
Initially only a limited amount of clones for each category may be assigned to your Space team. This can be increased by research. This will allow your clones to take less damage, and be upgraded from rank 1 to rank 5 - which will increase their energy significantly.
Aside research, Clones may be improved though rare special items such as Muscle Intensifier, Void Dust of Emptiness and others which will further improve specific clones with extra effects and stats. These items will generally be found in Space.