Placing Enemies/Objects on Tilemaps

While working on a tilemap editor I wondered how do professionals include enemies/larger objects into their tilemaps effectively. (I am always playing adventure snes games, and I still don't see an easy way to do it). It's very simple to create a grid of tiles that are all the same size and that works for most things but that still causes some problems.

The two solutions I have thought of to deal with enemies etc is to either include a smaller tile version of them that will only be used in the editor and then change it in the game engine. Or to put all of the different enemy sizes in different textures (eg. all 64x64 enemies in 1 texture), and then import it into the tilemap that way.

Are there any other methods that would make handling all of these custom objects in the tilemap editor easier that I have not seen? Obviously placing each boss/enemy separately in the game engine isn't really a solution.

It doesn't have to be professionals, but I would really like to know how some of you handle larger/movable objects in editors. I am sure people have more experience on it than I have :P
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