How do i link invoices to a paid amount, i received payment before the cheque was created and now i have deleted the original invoices and created new help please .....

When you receive a payment, then do not use an invoice, use a sales receipt.  An invoice is for when you are charging a customer an he will pay later.

As far as paying your supplier's invoice (your bill) you pay it when you wish, it has nothing to do with when you receive a customer payment