Data Persistance, Resources and AssetBundles

So I'm creating a game based on user created content. In the game, users will be able to create maps made up of tiles and various other objects. At present, I could use the Resources folder to store all my tile assets, but I'm wanting to make sure that I can add DLC via asset bundles later. I don't know if loading all of the assets (because I'm expecting there to be alot) via Resources.Load at startup is going to be worth while. For starters, I don't really know what the difference will be between loading all of my assets up front, and creating a data structure object to hold references to all the prefabs will be. I also don't know the best way to reference my resources whenever I save the data to a file. The individual objects will have little to no information as to where it came from, be it AssetBundle or Resource folder. I'm really just trying to come up with the most efficient way to structure my program to make it extendable later, and I'm just problem solving in circles right now and driving myself crazy.

I don't suppose anyone else has done this before and knows a good way to structure data persistence with creative content and DLC? Any help would be appreciated; I'm going to drive myself insane trying to solve this.