Should the total withholding amount on the Tax Withholding by Quarter section equal the sum of my W2's? If not, is was it determined?

It depends.

The amount listed on your tax return could be comprised of other withholdings on other sources of income including retirement, Social Security, or other investment sales.  

I recommend first going back into your entries for your wages to ensure you have entered all of the amounts correctly.  Be sure to check all of the input areas to ensure you have entered all W-2 forms correctly.  Pay specific attention to boxes 2, Federal income tax withheld, and box 17, State income tax, to ensure the amounts entered into the program match your W-2 wage statements.

If these amounts match your input, you may have other income sources such as form 1099-R for retirement that also have withholding amounts entered.  Compare your input to these forms as well as any other income sources that might have withholdings entered.