So although I can't answer many of your questions I will tell you I went on live chat with them and they sent me an excel file called QBOP payroll template. I filled it in and they made the changes on their end.
As for this year, when and if this happens again.. I am not sure at all what I should do to fix it. I was lucky that it only affected our employer remittance (although my accountant told me we did overtax our employees and they will get it back). I am not sure what the right answer is but I will be entering paycheques in on service Canada's calculator before submitting payroll once we get close to that $50k this year.. if that happens with all that is happening in the world. Good luck! Definitely talk to them again and tell them it is their problem and you need them adjusted.