If you decide to go for Manifest Destiny in the same playthrough, ensure you make a back-up save just before taking the last faction. Note: I did this in the same playthrough that I used for the achievements Kingmaker & Manifest Destiny by making use of the extra save slots. This guide focuses on how I did it using the Swadian Knight, however it is possible with troops from any faction.
There is no set way to achieve this other than the objective is to defeat all other factions. The best way to avoid this is to keep good relations with Lords or capture the kings and lords before taking the last castle/town. *This achievement can be a little glitchy, as you can control every town and village in the game but have a non-surrendering king who will completely disappear from the game until one of their vassals conquer a town/village. Empress can be achieved with either The Golden Throne or Manifest Destiny Just ensure you choose to play as a female when setting up the character.