When filing a Form 5329 to request a penalty waiver, should the penalty payment be made as part of the 5329 filing or as part of the 1040 extension filing in April ?

I missed an RMD from my IRA in 2018. I am filing a Form 5329 to request a waiver of the penalty (50% of the missed RMD). My plan is to file the 5329 prior to filing an extension in April 2019, anticipating that the IRS will make a decision prior to the final 1040 filing. I also plan on paying the penalty upfront. My question is whether the payment should be made as part of the 5329 filing or as part of the extension filing in April.