From what I'm reading, it only applies to users of the EFTPS website.  

So if you are paying through QBO Payroll, etc., the process hasn't changed except that now you will need to go on to EFTPS to change your password every 13 months.  

We have a few client's whose deposits we make through QBO, but most we make using EFTPS.  This is going to be a nightmare.