Most programs enable you to model several different compounds at a time, to move them independently and to toggle them in and out of view. A good way to compare different conformations of the same molecule is to least squares fit around a core part of the molecule. Most programs enable you to colour molecules in different colours so that you can compare overlapped structures. Once you have constructed a molecule you will need to store it in a file so that you can use it again. Modelling programs usually support several file formats, although one is usually a default of the system.
Most file formats contain similar information.
See if you can work out which fields store the above information. In module 1, you learnt the basics of unix and file management. These are important skills in Computational Chemistry and modelling.