All Model Options are stored in the DesignBuilder dsb file and so any changes you make to the model configuration will not affect other models.
You can open the Model Options dialog by:
All Model Options are stored in a single dialog but the options you can access depend on where you are in the model hierarchy.
Some model options are stored at the site level:
Most model options are stored at the building level:
and some are stored at block level:
So if you open the Model Options dialog when you are at building level you will not be able to access the Block Model Options. Likewise if you are at site level you will only be able to access the Display and Drawing tools tabs.
See also the Program and Model Options tutorial