Hi!
Indeed Game Master mode currently support levels with 1 region. If you developing a level in the editor i would suggest you to separate it in a few smaller levels - so all of them could be re-used with a different purposes. For your situation with second floor in building you probably would like to have it as separate level because in case you will need to make different states of that story - you could add them without dragging addition floor to it. That second floor with could also be used as "second floor" template for other situations you may need in GM campaign. Don't try to create all levels in the editor immediately suitable for your GM campaign. It much better to think of them as of generic level templates different GMs can re-use in their different adventures. Keeping levels small will allow you to reduce loading time and keep story modular together with having control of players party in a way of where they will go and when.
Small maps is one of the main comolaints about GM mode. This comment was disapointing to jear for me.