It's much easier to run Mystical Dungeon when the entire party is together. So when the characters decides to split up by going down different corridors, you can simply have them all end up in the same dungeon room. But if that sounds a little to simplistic to you, you can try one of the following advanced rules. Just keep in mind, you'll be running multiple games in different dungeon rooms.
In this scenario, the separate party ends up in different dungeon rooms. Everytime they enter a new dungeon room, a chanced roll (percentage die) is performed to see if it is the same dungeon that the other party is in. There is 50/50 chance that the separated parties will regroup.
In this scenario, once the characters split up, they will never meet each other again in the dungeon. The only time for a possible regroup is when they end up in the host lair; there is only one host lair room in the entire dungeon. The party that gets to the host lair first can stay there and wait for the other party.