I use invisible collision meshes a lot. For the overall walls and such it doesn't matter but for high(er) pol stuff laying around collision meshes help a lot. Don't just limit yourself to boxes; use low-res versions of models to get collision meshes which are faster to process than the visible model but which are still the same shape.
What I do is include the collision meshes as separate objects with alpha set to 0 in the b3d file when I model the level. Then when I load the level I set a collision mode for the collision objects but not for the rest of the level. If your tools can't do such trickery with b3d files then just save the collision meshes as a separate file from the rest of the level; if you build the collision meshes on top of the visible level and simply export them separately everything should load in the correct place.
What I do is include the collision meshes as separate objects with alpha set to 0 in the b3d file when I model the level. Then when I load the level I set a collision mode for the collision objects but not for the rest of the level. If your tools can't do such trickery with b3d files then just save the collision meshes as a separate file from the rest of the level; if you build the collision meshes on top of the visible level and simply export them separately everything should load in the correct place.