While both of these methods track money movement between two parties, they are quite different in their complexity. The decision to use one or the other depends on many factors, such as:
Are payments made as a one-time single payment or a monthly draw?
Is retention involved in the Contract?
Will you allow your contractors in your system to post amounts?
Is there an approval cycle involved in the payments?
Are unit price items involved?
The Payment Requisition module is much more complex than the Invoices module. Payment Requisitions is designed for the monthly payments against a Contract where retention is typically involved. You can track and pay based on an unlimited number of Payment Requisition Line Items (Pay Items). These Pay Items can be lump sum or unit price items. Unit price items can then be managed using the Materials module to track materials received on a project and post against a Pay Item on the Payment Requisition.
The Invoices...