After you file

I know it is right to wait until the original document is processed. However, it is almost April 18th and I dont want to wait over the deadline and have to pay the penalty. I realized there are two 1099 that I forgot to file. Originally, there is a refund that they need to pay back. After these two 1099, I owe some tax but it is much less than what they should refund me back. Should I amend it now and pay what I owe? Or should I wait until my refund is processed and then amend it? I do not want to pay any penalty for those two 1099 :(