Payroll/accounting software that allows one to easily input/import employee hours

At the moment, I run a business with ~200 employees. We work at locations all over my state, and they all have different rates - some of our employees have 10 different rates for different shifts each payroll period! Doing it this way is integral to our business. So far, Quickbooks Online is such an absurdly slow piece of software, it takes several days of full time work for our staff to process payroll.

I can easily write a VBA or Python script to export the raw data into any standard format - if there was a decent piece of accounting software that allowed an easy way to automate or input employee hours and information, I could do payroll myself in an hour. We're a business that rely on having a tremendous number of employees - software that charges per number of employees is out of the question, as the price is ridiculous for a company of this size.

Is there any (Canadian) payroll software that would allow me to either import raw data, input employee rates and hours quickly, or otherwise make this process less tedious?

To be frank, I'm actually a bit confused as to why Quickbooks Online seems to be commonly used - it may very well be the laggiest and buggiest piece of software I have ever tried!