After you file

If I wait after April 18th to let the original return be processed, will IRS assess a penalty regarding the charge that I owe due to the amended amount? 

 

Originally, I had a refund of $5000, which I still have not received yet. I amended the return (have not submitted it yet) and I should pay out  $3000. Should I amend the return now and pay the $3000? Or should I wait until the original return is processed? I just don't want them to charge me penalties on the $3000 if I do not pay them now.