MotionBuilder provides the following methods of merging an .fbx file with the current scene:
Both methods let you select the assets, setttings, and takes that are merged, appended, and replaced.
When you merge scenes with animation set on multiple layers, keyframes set on the BaseAnimation layer are merged (but not plotted) to the BaseAnimation layer. However, other layers are added to the scene as additional layers and these layers are not merged. The result is the same whether you merge-append or merge-replace the scenes.