If you place a mesh, the very first property on the property editor is gravity. Gravity always brings it to GROUND level, but since there is no ground it makes the object fall really far. That's one thing I need to fix in the next version. For now, turn gravity off for each mesh you place and explicitly set its Z coordinate to where you want. I know it's a pain
I haven't looked into differences between indoor and outdoor zones yet. Ambient sounds are one aspect and ambient lighting is another. For instance, you'll find that your dungeon zone responds to day/night cycles. Letting you differentiate between indoor and outdoor zones is simply one more thing that has to be done.
WC