"Pro Series won't let me e-file with a W-2 with zero tax paid in"

I dont recall seeing a place to enter the "tax" on a W2 that would prevent Efiling.   Youd mark it as 1 W2 with the 941 and 940 boxes checked then file the late payroll reports like IRonMaN stated below.

With the QBI thing now, not sure you can just throw it on a 1099 like that, can you?

He got a net check for $50,000.  You need to at least gross it up for Social Security and Medicare ————— and then file the late payroll tax returns.

You don't have a sole Owner. You have a Shareholder-employee. There is never a 1099-Misc from your own corporation to yourself, when you are the person doing the work for the business. You are the employee and get a W2, along with the K-1 that is related to your ownership position.

This person did not take $50k compensation. They simply took money, so it is time to turn that into compensation as taxable wages for 2018. Both the corporation, as the employer, and this person, owe taxes that are supposed to be part of the payroll reporting. Don't overlook FUTA and SUI.

Do a search...this topic has been beat to death in the forum.

The technically correct answer is NO, you can't.