No mod works for replacing factions; only Haven can be replaced. With the others, you download them, put them in the folder, and only the castle's appearance changes.
Do you have any other mods installed?
Here's an example from my friend - he installed the MCCS and NHF mods, and then put an old mod on top to replace the Dungeon, and as a result, only the external and internal appearance of the castle changed, because in MCCS\NHF they change the creatures\heroes of the Dungeon, but they don't change the city itself.