Tile Based RPG Resource Management and Loading

I’ve started work on a Tile Based RPG (Link To The Past kind of deal). The way my world is setup is that I have 3 or 4 levels, and within each I have a bunch of areas that are free roam. So, when the player moves off the screen it transitions to a new area, rather than having the screen scroll with the character.
I would like to ask about loading resources. As far as a tilemap goes, the layout of the tiles would be stored in a file, and loaded from that. That’s simple enough. What I’m unsure about though, is loading objects into the maps. Say collectible items, or objects the player interacts with. Are these items typically represented by tiles as well? I’m not sure how to handle this.

For example, say I have a Key class. Within the key class it has an ID of the door it unlocks. Say one level has some 20 doors to unlock. I could load these into the game the same way as tiles (via a file), but how do I decide which key is which and where it should go?

This question has gotten kind of confusing. Please ask for clarification if it is needed.