Hot Seat is not officially supported at the moment by Stardock. You could get hot seat working through the use of cheats.
After the cheat parameter is set up. 1) Set up the game as normal (with a civilization that second player wants to play) 2) Select a ship or a planet that belong to the civilization that the second player wants to play. 3) press ctrl+shift+z
To start the game immediately with a second player, one can use the ctrl+t cheat to teleport a ship to the civilization's homeworld and then enable ctrl+shift+z.
(Note: The second player loses some of the bonuses that the computer civilization had. The more experienced player should play as the non-default player)
(Note: To switch player in pseudo hot seat mode you will need to press ctrl+shift+z on target player's object everytime passing the turn. Click 'turn' button only when all players have made their moves.)