I amended my FedTaxReturn but isn't processed yet. IRS asked me to pay the amount + late penalty I will save with amended return. Should I pay amount until it's resolved?

I want to avoid paying penalties but there is no way to contact IRS to let them know that the amended return should make up the difference. What should I do: 1) Just wait until the amended return is processed (and risk more penalties) or 2) pay the amount now and get a refund much later. The amended return takes as much as 15 weeks to process.