Naming molecular compounds gave me some trouble, because I didn't know when to use the prefixes on the first element and when to use them on the second element. I'm not sure when, but at some point it just made sense; You use the appropriate prefix on the first element when it has more than one atom of that element. You use mono- on the second element if there is only one atom of that element, and if there is more than one of the second element you use the appropriate prefix.
To know when to use prefixes for molecular compounds, you look at the chemical formula. Molecular formulas are not ionic formulas. Most of the molecular compounds we are dealing with are binary, meaning there are only two combined elements. At the end of every second element, you replace the ending with the suffix -ide.
