Imperial Assault uses preconstructed maps, the idea of using Core Space's 3d terrain sure is exciting but I'm not sure how it could be done...
Well the first thing you do is think out of the box. IA uses pre-constructed maps because it comes with a limited set of terrain tiles that by definition constrains the player. Ignore all that and build yourself a cool looking board with Battle Systems, and simply modify any rules that are a problem.
Expand your horizons and change the game to fit the terrain not the other way around.
I've done it with their fantasy set to play a fully 3 dimensional version of Heroquest - great fun having my heroes need to fight their way up stairs and along battlements before descending to a dungeon and jumping a lava pit to obtain some piece of magical treasure. I've similarly seen it done with games like Space Hulk, Zombiecide, AvP etc.