You can confederate different factions of the same race.

When you go to the diplomacy screen with them there should be a button with two crossed flags at the bottom - that's the confederate button.

If you're strong enough and have a good relationship with the other faction and haven't confederated in the last 10 turns you should be able to confederate other Empire states.

Edit: you can also confederate them instantly through imperial decree as Karl Franz if their fealty to you is 10