How are names determined for Commanders when you recruit them?
All names are randomly generated, but you can rename your Commanders.
I have a commander at a base but it has no effect, why is this?
You must assign commanders to be Base Commander of a base in order for their effect to take place.
What exactly does dismissing commanders do?
It is just like demolishing structures or decommissioning fleet, though you do not gain any of your credits or XP back.
Do commanders use jump gates?
When you are moving a commander to another base, they use a jump gate if there is one available.
Note that you must de-assign a commander before moving them.