Semi-Auto Payment Reconciliation
If there are large no of Invoices that needs be reconciled quickly without manual allocation, Process Payment Reconciliation doctype can be used.

Steps:
First this feature must be enabled through Accounts Setting. Enable Auto Reconcile Payments in Accounts Settings.
Navigate to Process Payment Reconciliation doctype
Select Company, Party and Receivable/Payable Account for which Reconciliation has to be done. Save and Submit. Document will be Queued status.
A Background Job that runs every 15 mins will pick up Queued docs and will start reconciliation. If needed, the Job can triggered immediately using Start / Resume button.
This will create a Process Payment Reconciliation Log record with details on the Total No of Allocations that will be processed and the successfully reconciled entries.