What I'd for that is build some brush work around it so that you fit the 'terrain' to the building correctly and then convert that trisoup into a model. It's been a while since I did any QW or MegaTexture work but whilst you *can* use brushes for 'terrain' in the same sense that you could traditionally make terrain from brushes, it won't or can't be used for MegaTerrain as MegaTexture can't be applied to brushes in that version of the engine.
So basically you're going to be making a template to get positions correct, converting that to a model and then reimporting that back into the editor for MT use. With regards to the bounds of the level (as in the "turn back now or die warnings?) they're defined by an image rather than the model iirc. I'd have a read through the QW Wiki for info on that one.
You won't get much use from a top down view because the size of the final shot is only relative to itself, you won't know how many pixels width/height something is to use as a template without a lot of mucking about to figure that out. What you could do however, is if that building is 'regular' shaped you'll be able to directly translate grid units into Blender/3D app units; 256x256 Radiant units is the same as 256x256 Blender units for example.
Does that make sense?