How are atoms arranged in molecular compounds?
For covalent compounds:
consider drawing the lewis structure of the covalent compound in question, putting the atom which is least electronegative (save hydrogen) in the center.
Drawing the pertaining lewis structure of the covalent compound in question can give you a good mental picture of how the constituent atoms are arranged within the compound.
In other words, draw a lewis structure of the molecular compound in question to see how it's constituent atoms are arranged.
To draw lewis structures, count the number of valence electron about each constituent atom and place the atom which is least electronegative in the center of the compound.
Here are some examples::
Keep in mind, however that this is not necessarily the same in the case of ionic compounds, where the formula given is instead the formula unit (the simplest repeating structure within the crystal lattice) and not the molecular formula of the entire compound.