How do I unlock the second assault and guardian fortress in doomsday?

You need to earn speciality points and go to the speciality tab in the doomsday conquest event. Use the points in the blue section in the bottom section. As you work your way down you will unlock the use of additional assault and guardian fortresses.

Once you unlock them, place them next to the alliance centers. You can then respec your points to other specialities and still keep the buildings.