No, you should not put a stop payment on the check. As your return stands right now, the IRS expects that payment and stopping the payment may complicate things further.
Since you electronically filed your return and it was accepted by the IRS, you can amend it now. Also, there was no need to mail a copy of the W-2 with your payment since the return was filed electronically.
See the instructions below to learn how to amend your return.
https://ttlc.intuit.com/replies/7276605
