After you file

If you income qualifies you for the stimulus payments, a screen will come up when you review your return.  tt will ask if you received the first and second payment and any amount that you received,  Then it will apply those payments to reduce your income tax owed or to increase your refund.
IRS Stimulus Payments

If the screen does not come up automatically when you Review, there is how to bring it up manually:

At the top of your tax return select Federal Review
 

That will take you to this screen where it asks if you have already received your stimulus payments.  If you received the first or second payment already, then select Yes and fill in the information.  

When that page is correct, you refund will be adjusted correctly.

Irt