Command points are displayed in top right corner, you can also see a breakdown by clicking it. Command points are generated by colonies, structures and leaders. Each active ship uses up command points. You have to pay 10 BC per turn per every point you ships use up over how many you generate. This is meant to make supporting big fleets taxing.

Command point come from:

Ships eat up command points according to their size class:

These values can be modded.