The thing that helps me the most (though not exclusive to indoors maps) is to sketch out a rough concept on paper before starting. Place down key features that you want to include, figure out a rough scale for the number of tiles being used by chunks of the map to get a rough idea of what the map’s dimensions are going to be, and then block those areas out in the map program and adjust as needed for tweaks, height changes, etc.
Try to picture the flow that you want the map to have and the path(s) that the player will take through the map. Study other maps to understand tile shadowing and height mechanics.