Underpayment penalty -Paying directly ?

You don't pay that separately.  It was included in your tax due.  

And if the IRS determines a higher penalty, they will bill for the difference.  If the IRS determines a lower penalty, they will refund the difference.

Oh yeah, 1040 line 24 says Estimated underpayment penalty and is included in line 23.  Notice that line 23 is more than line 16-19.  Or you can even have a penalty when you are getting a refund.  I did once.  

will they bill even for $5 ?

my main question was -

Can I pay @ https://www.irs.gov/payments right now to avoid any sort of notice from IRS ?