Well, using a burrowed unit system, there are two ways you could do it. When you enter the building, or when a trigger tells the screen to move to some inside building, you set a switch or something.
When this happens you can either do it two ways. Using multiple players or a single player.
Using multiple players:
You know which room your moving the screen to, give the proper number of burrowed units to some other neutral player and center on the next unit. Then give the units back to their original player, keeping the screen on the unit it is centered on. Its simply a larger
Grid system.Using only one player can be done, but I would recommend using the give method, using an extended player if you must.
To do a single player method, you center a location on the first burrowed unit, and remove it, replacing it with a different burrowed unit. Repeat this untill you have the right unit to center on.
EDIT: Wait are you having difficulty trying to figure out which square the hero would be in? (Sorta like a zelda map where you cross over seamlessly.)
If so, you could use a larger grid on the edge of the map, like photon cannons or something, and simply use x/y counters to tell where the hero is.