build new floor v.s. auto generated wall height with added roof planes

[AaronS71188]

Apologize ahead of time for incorrect terminology, really dumb questions, scattered thoughts and vagueness. 

Im new to all of this and I'm not an architect, but my company is putting on an addition and asked me to help with the model. Need some guidance if at all possible because walls are not automatically generating correctly and the model is becoming a mess. There have been many additions to this building over the years which makes this a fun one. Many different ceiling heights, floor heights, levels, wall types, roof slopes, etc. 

 

I'm debating starting from scratch again to make sure things are done correctly out of the gate. 

If you add a roof and give it a specific height, the foundation wall (or floor 1) will extend up to that roof, even if the peak is at like 300" for instance. This is good in the warehouse areas where there are no ceilings between the slab and the rafters (warehouse shown as #1 in the image). No addition is happening there, so do you think it is okay to just keep this as 'one floor' and not try to stack two floors plus attic to be the correct heights? 

 

I want to have 2 floors in the area marked #2, and 3 floors in the area marked #3.. both are giving me trouble

it might be because im trying to draw the roof before adding second and third floor walls. I have those walls seemingly overlapping the auto generated attic walls. Then i have issues with deleting something that will cause auto generated things to become manual, which i don't think I want.

 

Should i build a new floor, derived from the first floor, then delete walls  that i dont need... or should I create a blank new floor and manually draw only what i want? 

 

My mind wants to treat these like 3 separate buildings because of all of the level changes, but chief messes things up and causes me more problems when i connect the walls of the '3 buildings' 

 

Probably extremely vague and all over the place, but any guidance on how to make this what I want is much appreciated. Go easy on me! 
 

[AaronS71188]

maybe this will help visualize the additions.. this is the existing structure as it stands today with some red marks of where things are being added. 

[rgardner]

Build the model how you would build it in real life.  The walls auto build to foundation and roofs and all heights are governed by floor and ceiling heights set in the room DBX if it is set differently than the default set for that floor.