You are correct. If your column features will be both exterior and interior you would group and assign them according to LEVEL>ELEMENT>LOCATION>CONDITION.
For continuous columns, you can slice them at the same height as where the levels split and then group/paste them into the appropriate levels. This won’t affect the drawings, but will make for easier organization (so no geometry exceeds the height of the level layers).
Hope this is helpful, sounds like you got a good grasp of how to use the plugin. This is a tricky one!