I think the sprite and the map should be seen seperately, You should however find out how to convert the pixel coordinates to the isometric-tile the sprite is on/touches, there is a library out there that has a large collection of Isometric function, including a pixel offset to iso-tile index converter!

I made a very simple isometric map editor a long time ago and I made the mistake of trying to treat the sprites as parts of the map, in the end this is unmanagable.