If you sent the check in with the 1040V voucher you don't have to worry about the payment. The IRS will send you the unsigned 1040 and request that it be signed and returned immediately. Since you did send in a payment you will not be assessed a fee for Late Payment. It is possible that the IRS will issue a Late Filing Fee if the signed return is not postmarked by April 18, 2017.
You should not send another Tax Return and payment.
