Geometry optimization of a small molecule inside of a larger one
I don't think you've provided nearly enough detail about your problems, particular "a".

But let me comment about "exporting from ChemDraw." Keep in mind that ChemDraw is a 2D tool. Consequently, the lengths between atoms are designed for depiction on paper, not necessarily for accurate representation of the 3D geometry necessary for calculations.

Avogadro can import 2D geometries from ChemDraw and attempt to assign reasonable 3D geometries. In your case, this seems especially troublesome since you want to have one molecule inside another.

I'd either:


Sketch the two molecules separately in ChemDraw and then use Avogadro to "insert" the smaller one into the larger after geometry optimization.
Use Avogadro to create the full 3D geometries of each molecule and then, select the smaller molecule and use the manipulate tool to move it into position.


As several people have commented, if you want to preserve the appearance of bonds, XYZ is not the right format. It only stores coordinates, not bonding information. Avogadro and other tools will attempt to re-perceive bonds and bond orders, but this is not a perfect task, particularly in the presence of multiple nested molecules.

Instead, I'd keep a file in CML format with the bond orders intact. This is more-or-less the "native" file format for Avogadro.