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Here's my exchange with the FTB chat representative:

Question:

RE: Quarterly estimated payments for 4/18 and 6/15 -

Should I use the voucher for each date and write a separate check when paying prior to the 10/16 deadline, write one check and attach both vouchers or something else?

Answer:

You can do either way, you can send two separate payments for each quarter or one total payment using only one of the payment vouchers.

Due to the extensions we will apply the payments accordingly when we receive the payments.