Try the IRS web site.
https://www.irs.gov/individuals/tax-withholding-estimator
From your description, it sounds like QBSE might be calculating the total tax you are likely to owe. You would then subtract out your wife's withholding to arrive at your estimated payments. However, it also sounds like QBSE is not asking about dependents or itemized deductions, which is pretty important.
I don't think anyone on the Turbotax forum will be able to explain Quickbooks for you, I think you need to go back there and find someone else with a higher skill level. Alternatively, there are one or two users here who might have more familiarity with QBSE.
@VolvoGirl @Critter-3
