I am having trouble building a model. The geometry of the model is not displaying correctly or Chem3D will not allow me to build a model because of missing atom types.
Chem3D builds models based on the information in the Atom Types table. There are a number of atom types already defined in this table, but there are too many variations to define them all. Therefore, it is up to the user to define atom types as needed. If the geometry is not turning out correctly, then you need to define atom types with the correct geometries for your model. Please see the manual on defining new atom types.
Turning off the Building Preferences will also allow you to build models with undefined atom types, but you will have problems running MM2 calculations in this case.