Basically I want to make a quest line similar to Assassins Creed where you can improve certain areas by meeting specific criteria and then invest in them. You already do this on a small scale with player owned houses by becoming a thane, buying property and paying for improvements. Because, when editing player houses you can see everything in place for all the improvements at the same time.

What I want to know is how do I set it up in the Skyrim Creation Kit so that specific triggers change one creation to another?

So an example would be... Clearing Helgen of Bandits and an Architect shows up camping out saying that now that the bandits are gone he could rebuild, but he doesn't have the funds. Hence if the player can supply the funds worker npc's show up "building" and over a period of time buildings are rebuilt until Helgen is a functioning town again.

I suggest you watch or read my tutorial, In essence you enable/disable Xmarkers that have children linked to it, as children take on the properties of the parent!
http://www.gamesas.com/topic/1346963-tutorial-custom-house-upgrades-via-npc/