a) The formatting difference is because the automatic numbering uses the format from the title. The first example you use has the (correct) title format "11.2: Ion-Dipole Forces" while the second one has a - instead of a . : "14-4: Integrated Rate Law" Fix the title and the numbering format will be consistent.
b) I can only answer this partially: Yes, you need a label because that is how the equation is referenced. So for example: \[ E=mc^2 \label{EinsteinEq} \] To reference this equation you have to use the command \ref like this: See equation \ref{EinsteinEq}
Someone else will have to answer the part about referencing across pages, I don't know.
