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@johnicahorton wrote:

What can anyone tell me about how the penalty for not having paid in 90% of tax works (as distinct from penalty for not paying quarterly estimated tax payments)? 

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It is not distinct from the estimated tax penalty.  They are the same thing.

If a taxpayer did not pay at least 90% of what they owe (see note below), they SHOULD have made Estimated Tax Payments (or had higher withholding).  So that is the Underpayment of Estimated Tax Penalty.

As you read the instructions, it is more complicated than that.  Factors include if you owe more than $1000, what last year's tax was, and higher income taxpayers may need to pay more than 90%.  But the bottom line is that you are referring to ONE penalty, not two different ones.