I use 3d Software like Blender or 3dsMax all the time for asset creation. Some scenes are easier described in 3d Software than in AGK.
I have written a 3dsMax script that exports the whole scene to AppGameKit, as single objects including a list with their position and rotation lightmaps, texture names, shaders and so on.
but the regular workflow should be:
1. Create models / Export to engine format (fbx for example)
2. Load models in level editor (or some placement function in the engine itself)
3. Create levels with the level editor
4. Load created levels in your engine