basically to get an underground area you lower or heighten the terrain somewhere on your map.. you put some doodads like rocks there, use page-up or page-down to let them float, you then press enter when selecting those doodads.. make it so that it ignores pathing and has no doodad footprint that way your units can move underneath it, and it allows you to position it on any coordinate rather than in a roster. I am currently trying to make an underground area for my own map. It's rather hard finding a proper doodad that won't look really ugly if you are trying to cover up large areas. As to how to make enterable houses, you should search the forum there was something with a footprint on this forum telling you how to do this.
I worry that functionality for this might be.. removed. Because before the beta they said that this was going to be the 'first rts to prominently feature a subterrainian layer', which sounded awesome. (they were talking about a REAL underground later, not burrow or anything). But that clearly did not come to fruition, or at least hasn't yet (who knows with release, I guess). :/
Please not! How can they remove something great then this? I doesn't know that they said it would be able.... but if they said... how can they remove this?
Maybe there is still some hope because they said they won't say anything about "indoor zergbuilding" so maybe this means "yes there will be" and so it could be that also indoors and tunnels are supported.
Wow this will add a whole dimension to the SC2-Galaxy ;)