Per Gym level (see expanding level) you get three skill points. Free skill points are shown with a digit on the grey flag, on the left of the menu where the training symbol is.
You can dispense skill points to every unit which you have unlocked. Every unit has three skills you can improve by using these skill points:
Damage, health and healing (resurrection after a fight). Each skill can be improved up to 25% by spending skill points.
Confirm your distribution by clicking the “Save distribution”-button. You are able to reset your skill points at any time. You will then be able to distribute them anew.