Best practices for pay period begin and end dates

We will be process payrolls for some of our affiliates.  Each affiliate will become a process level in our HR company.  Our current biweekly pay period begins on a Monday and ends on Sunday at midnight.  

We have not determined if the affiliates should be moved to our biweekly pay period begin and end dates or if we have more flexibility if affiliates pay periods have a different begin and end day. 

We would appreciate any comments on what setup has worked well or should have been done differently.

Thanks for any guidance you can give,