Each Base has only one Commander, which can be sent with both gathering and attack marches. The Commander cannot be killed, injured or captured, regardless of the result of the battle he is sent in.
Every time you complete missions or take actions which give you Experience (XP), the points are added to your Commander. Commander XP can also be purchased from the store with Gold.
For the time being, you can upgrade your Commander up to level 60. All extra points that surpass level 60 are stored, even if they are not shown in-game. Leveling up will bring your Commander more Skill Points, which you can assign depending on your strategy.