The payment you make now cannot be assigned to a specific quarter. You only need to make one payment to the IRS and one payment to the state. Both payments will be applied to your overall taxes paid, but you cannot go back and say this payment was meant for the first quarter and this payment was meant for the second quarter. Payments are applied in the quarter they are made.
If you do receive a penalty you can file form 2210 with your federal taxes to request the penalty be waived. This form is found by clicking>> Other Tax Situations>>Additional Tax Payment in TurboTax. If you file this form you will need to print and mail your return as it cannot be e-filed.
For your Michigan state return, if you incur a penalty, you would need to Request a Penalty Waiver from the state by following the instructions in the link.
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