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"which have to do specifically with payroll taxes I alrea...

"which have to do specifically with payroll taxes I already paid for 1st quarter 2016."

Which means you already have the Accounting data, so again, this is a Not Affect Accounts scenario.

"Because I was just using an Excel spreadsheet to calculate withholding amounts, I never realized until now, that YTD income, and county of residence can change the withholding amounts over time."

Well, they don't. YTD is Accumulation. There are taxes that have Wage Limits, such as FUTA stops at $42 for $7,000 of wages. Is that what you mean?

County of Residence seems like a Local Option tax for specific wages?

"So, long story short, I'm pretty sure I under-withheld from my employee's paycheck this entire time."

Well, it's a bit late to try to collect from that person and send it in. Your Reporting should have brought up any issues.

"Naturally I've arrived at this assumption because the dollar amounts my accountant had me pay in payroll taxes seem to be more than what I withheld - woohoo for me - lesson learned."

Are you overlooking that the Employer pays a share?

"Question:  Now that I have all of my employee YTD info entered correctly, how do I enter the YTD payroll taxes which I have already paid?"

You already have it, as banking entries and expense entries. Your previous payroll would be:

Gross Wages + employer share of taxes = Total Payroll Expense