You don't need to do anything special, other than to wait until you've already received your refund before you mail in your amendment with payment.
Once you have your refund, the money is yours to spend as you wish. There's no need to wait until your amendment has been processed, which can take months.
When you mail in your amendment, include a check or money order for any owed tax. You can also pay any federal taxes due at the IRS website.