I have all payslips entered and printed, etc. - pay ending was October 29, 2016. Cheques were written November 1, 2016. How do I enter the payment to each payslip?

If you did everything in straightforward fashion, when you created pay slips, that posted the amounts to Employees clearing account, a liability account (since the business owes the money to the employees). When you are ready to pay, under Cash Accounts tab, Spend money. Allocate each paycheck expenditure to Employees clearing account and the Employee involved. This will credit the cash account from which you are paying and debit the Employees’ subaccounts under Employees clearing account, zeroing it out.

The Spend Money would look like this

thank you - will try this