Do I misunderstand? I'm unclear on why you need to make estimated payments if you also have a job that has withholding.
Let's say you are an independent contractor, and you are responsible for making quarterly estimated payments (not "quarterly withholdings"). You can be penalized by both the IRS and the state if you did not make estimated payments each quarter, that matched your income in that quarter, even if you paid in full when you file your return. However, if you paid in full now, then the penalty for missing the April 15 payment (for example) would be calculated for 9 months instead of 12 months; the penalty for missing the June 15 payment would be calculated for 7 months instead of 9 months, and so on.
You will also want to use the annualized income method to compete your penalty on both the federal and state return. Look for penalty interviews under the "special circumstances" tab if the program does not prompt to to run the penalty on its own. The annualized income method shows your income for each quarter, your payment for each quarter, and calculates the penalty (if any) based on what you owe for the quarter, rather than assuming that wages and payment are both evenly spread out.
