The RRG says that in the command phase, you place order tokens next to units that are commanded. Then in the activation phase, the order tokens are flipped after the unit is activated.

Do only commanded units activate? I'm not understanding how the rest of the units that aren't commanded can activate, as they aren't issued an order token during the command phase.

The rest of the tokens that aren’t ordered are put into a bag or randomized face down. When it’s your turn you can either choose to activate a unit that has been issued an order, or you draw from the random pool and issue an order to a unit that matches the type on the token.