Employer paid tuition after I gave them the money

There is no way to "show that" on the IRS forms nor is there a reason to show it.  You just need to enter your info in such a way that TurboTax (TT) recognizes the correct amount.  The simple thing to do is just leave box 5 blank when you enter the 1098-T. 

The 1098-T is only an informational document. The numbers on it are not required to be entered onto your tax return. However receipt of a 1098-T frequently means you are either eligible for a tuition credit or possibly your student has taxable scholarship income. You claim the tuition credit, or report scholarship income, based on your own financial records, not the 1098-T.

If you claim the tuition credit, you do need to report that you got one or that you qualify for an exception (the TurboTax interview will handle this).

Alternatively,  in the 1098-T interview, you will also reach a screen that allows you to adjust the scholarship amount for "amounts not awarded for 2021 expenses".

Yes, you can correct this by reporting the amount as paid by you.  If you are ever questioned, like your employer stated, you can explain the situation and provide receipts.  It would also help if you had a copy of the agreement for you to pay employer and employer pay University in order to receive a discount.

However receipt of a 1098-T frequently means you are either eligible for a tuition credit or deduction.

If you claim the tuition credit, you do need to report that you got one (the TurboTax interview will handle this) but use the financial information that you have to claim the deduction.

Main point is to just keep records.

@wahootree

If your employer paid your tuition with pretax money, then you cannot get a tax deduction for it since you never paid tax on the funds.  It will be seen as a fringe benefit even though you gave the employer the funds,