I was hoping this would get some responses; been trying to figure out the same thing for a while. From what I've gathered you need 2 editors: 1 for rooms and 1 for your mini-map. Rooms must be built in both, side-to-side. Each time you create a room in the mini-map, give it an ID, then create a tiled BG or something and stretch it over the room in the other editor and give it the same ID. When the player overlaps that tiled BG and its ID matches that of a room on the mini-map, set the "highlighter" and scroll position to that room on the mini-map and whatever else.
Another way is to use a level editor and build the entire area in a single file - yes, all of Crateria in one file - and generate the map automatically based on that data (Using Tiled BG objects stretched across each room, each with their own set of variables, door positions and type, etc...)
Aside from that you might want to ask DoctorM64 (creator of Project AM2R - Another Metroid 2 Remake) how he did it. I'm pretty sure he released a .gmk of his mini-map editor and some other stuff somwhere, so if you know GML, even a little bit, that might help.
Keep us updated!