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(edited before any replies to clarify the question better with more brevity) 
[-  macuser_22  -] replied with excellent detailed answer but I'm confused specifically wherein his efile method (using manual Forms fetch and fill) said, 
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Enter the forms mode and click on open form. Type in 5329. Choose 5329-T for the taxpayer . . . . . .Scroll down toForm Part IX line 52 and enter the RMD amount that should have been taken. On line 53 enter the amount of the RMD that was actually taken (probably zero if it was missed)  . . . . . . . . Then click the "Explanation" button and enter the reason for missing the RMD and your statement requesting a waver.

[-here-]->You will not pay any penalty now until the IRS determines if it will grant the waver, then they will inform you if you owe the penalty.<-[ ? -]
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But then in the quote from Form 5329 instructions it said. 
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3. Complete line 55 as instructed. You must pay any tax due that is reported on line 55.
The IRS will review the information you provide and decide whether to grant your reques for a waiver.
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The two methods wording seem confusing whether you have to pay the tax before or after the waiver is determined OR is it to be interpreted that you pay the tax with the Efile or Postal mail and wait to see if you get a refund?