If you use a payment method code set with a Balance G/L account or Bank account in a sale or purchase invoice, when you post the invoice the system posts also the related payment In one step.
The invoice and the payment are closed and applied.

If you choose to use the Sale or Purchase Journal to post the Sale or Purchase invoices and you use the same method code set with a Balance G/L account or Bank account, the system does not post any the payment when the invoice entry is posted.

This feature should be used also in Sale or Purchase or G/L journal on posting the sales or purchase transactions.