When the client makes the payment on the IRS website, ss it okay to process the extension even though it says Paper Check?
I am likely over thinking this. I'm almost certain that the IRS will match the filed 4868 extension to the payment from the web and determine the actual payment amount to apply to the tax return.
If your client pays over the web by Direct Pay or credit/debit card, the payment is registered on the date of payment and it would be treated as an application for automatic extension so long as that is the payment type chosen. Your client should retain the acknowledgement and send you a copy.
There's no need for you to e-file another extension. Not sure where the paper check comes in though...
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