Just because the client extended the return, nothing has changed.  File the return like any other that you have filed.

Iron Man Is Right. Same thing goes for the exact opposite which happened to me this year, I.E. I filed the extension but the client chose to prepare the return themselves.

IRS has the extension, you just need to file the return.  If they sent a payment with the extension, you can include that payment on the Tax Payments worksheet (Line 9) and it will funnel it to the line on the 1040 where it belongs.