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.
Clones Sky Team
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.
Clones in Space
Upon unlocking space, clones will be usable in space fights. Unlike for Sky, each of your 4 Space fleets will have its own contingent of clones.
Once marshaled in a contingent, a clone cannot be withdrawn and cannot be moved to another fleet. You can, however, assign other identical or different clones to other teams if you have them.
The number of clones you can assign to any fleet depends on multiple factors:
Airship Ranks : Each of the Airships assigned to each fleet allows 2 Clones per Rank of the Airship (up to 12 each)
When a ship is said to increase clone capacity by Y, the following actually occurs:
Lower clones capacity increases by Y
Higher clones capacity increases by 6/16 * Y
Super clones capacity increases by 1/16 * Y
All deployed fleets must always be able to support assigned clones. This means you cannot remove a ship from a fleet if it would reduce your clone capacity below the current amount in the fleet. When a fleet is not deployed and sitting at Eden, you CAN remove ships from the fleet that would cause the clone capacity to be below current amount in the fleet. You will not be able to launch the fleet until the capacity is high enough again to support the current clones. You can use this feature to shuffle airships around to meet certain stat requirements.
During Space Combat, the clones in the team can get damaged if you end the fight with less than full Energy:
Lower: May suffer damage, if Remaining Energy < 95%
Higher: May suffer damage, if Remaining Energy < 65%
Super: May suffer damage, if Remaining Energy < 35%
Initially only a limited amount of clones for each category may be assigned to your Space team. This can be increased by research.
Research will also allow your clones to take less damage, and be upgraded from rank 1 to rank 5 - which will increase their energy and special skills significantly. Clones do however also cost significantly more to produce at higher ranks. New clones created at the Cultivation Hall must always be of the highest rank you can produce. Clones created before learning a new rank can be upgraded at a cost (less than the production cost).
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.
For detailed info, enhancing and where to get each clone gene see their individual pages. Clones with Green backgrounds are temporary clones from Space Analsysis.