Hello Corey!
1. Modifying the drawing set will not affect the scenes you have already created using the ConDoc Tools. I would recommend deleting the scenes and then recreating. I usually do a fair amount of testing before I commit to using on a project.
2. Section Plane height controls where the active cut will be placed above the finished floor level. So if you enter floor levels of 0′, 10′, and 18′, and your plan cut is set to 4’… The active cuts will be placed at 4′, 14′, and 22′. Once placed you can manually move/adjust the active section planes.
3. Not sure I understand the question, specifically the hierarchy of folders? You can set the viewport names to whatever you like… This will eventually find it’s way to the scene name.
In my experience, objects showing up where they aren’t supposed to is a tagging issue. Is your furniture properly tagged? Feel free to shoot the model and drawing set over to me at [email protected]… or upload here https://workdrive.zohoexternal.com/external/anTTQ2LgatB-Kd8U0