In general, it is best if you pay any estimated taxes for next year separately from the current year's tax payment.
When both payments are submitted together, they seem to all be applied to one year or the other. What works best is to send the payments separately, with each one clearly labeled with your social security number and the year to which the payment is to be applied (both on the face of the check and on the voucher that is sumbitted with the payment).
