Hello Andy!
There shouldn’t be any issue with what you are describing. When you run the plan generator, make sure you check yes for a basement. This will create a Level_00 layer. Assign this layer to the group holding everything that represents your basement. When you create a foundation plan, You should see both the Level_00 and Level_01 foundations turn on (not 100% sure without testing). At this point you can start to manually adjust scenes as desired, turning layers on/off and updating the scenes. Just be careful you don’t mess with the scene cameras! Let me know if this helps!
Mike