The methodology depends on whether or not you had taxes paid/withheld per a W2. What I've read before is if you had W2 tax withholding the IRS just uses the April 15 tax deadline to calculate under payment penalty. If you pay estimated taxes they could use each of the quarterly estimated tax due dates. I can't link a source for this info; it's just what I recall. Hopefully someone else can give an actual info source.
