Let's assume that it only became clear to me during the last quarter of tax year 2015 that the tax withheld from my paycheck etc. was quite a bit less than what I owed. I could have filled out form 1040-ES and mailed in what I owed by 04/18/16 without having to pay penalty, interest ect. for underpayment, right?
If I am wrong, what should I have done once becoming aware of the underwithholding in order to avoid IRS penalties etc.?
No. The estimated tax payment for the last quarter of 2015 was due January 15, 2016, not April 18. If you didn't pay it until April 18 you were three months late and would owe a penalty and interest.
Even if you paid it by January 15 you might not have avoided the penalty. The amount you have to pay during the year is due each quarter. You can't pay too little all year and avoid a penalty by making a big estimated tax payment at the end of the year. If you did not pay enough through withholding or estimated tax in the earlier quarters, you could still owe an underpayment penalty, even though the total for the year is sufficient.
What you should have done was greatly increase your withholding for the remainder of the year, so that the total withholding from your pay for the year would be enough to cover what you owed, even if that would mean having most or all of your pay withheld for taxes. This works because, unlike estimated tax payments, withholding it treated as if it was withheld evenly throughout the year, even if it really was mostly withheld in the last quarter.
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