Terrain just does....

Hi, Im having problems with my game atm due to the terrain editor not being able to do what I want it to.

Briefly what I need is buildings underground where walls and roof are part of the terrain but also allowing more buildings and terrain on top(and around) of these structures, and again on top of that I want the surface terrain with more buildings on that, also I need a better way of tunneling through landscape, cutting holes in things is not a viable option and I don't want any make-shift ways of doing this because they all have problems for example cutting holes in terrain gives a graphics bug where you see the landscape when you should not(even if it worked properly it would still not do what I want it to)


So my question is are there any other world editors that people are using or is it just that the game engine is limited on what it can do?

I would appreciate any help on this because it is vital to the creation of my game.


Thanks in advance

Steve