What value do I put in the Form 2210: Line D Withholding---put a value in the provided box fixes only one value in Part II, Line D and there are only 3 columns???

It depends. Your withholding taxes for your federal return go on Form 2210, Part I, Line 6.  TurboTax will automatically carry this number to your form and in all the appropriate places. Likewise, any estimated taxes would carry to this form based on when paid in your entry, if applicable.

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People complain there are three boxes not four.

Are the three boxes labeled?

@KRSolomon75