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Go to Fleets screen and click one ship after another to fix them one by one.

Also, when they are on automatic routes (autotrade, patrol) and they visit a port on the way, they repair automatically.
 
With the latest patch you can also select "repair fleet in port" from the commander info window (click commander face in 3D map mode to open fleet info, then select commander face and there you have it). This makes the fleet repair itself automatically everytime it visits a port.

Note that not all ports have shipyard (=required to fix ships) and that in some cases repairs can cost A LOT of money, so you might want to be careful to avoid running in banktrupcy.