Hi Helentroy.
Thanks for contacting the Community.
If you wanted to add the payments as essentially unallocated credit to the customers account through the banking page, there would be a nice easy way of doing this.
Essentially you would select the payment in question from the banking page and click onto it, this will open up the details of this transaction. If you then select the account as the DEBTORS account and record the customers name as the appropriate customer you will just be able to click ADD at the end of the line. This will record the value of the transaction as a credit on the customers account that can then be applied to future invoices when you create them.
When you have created the invoice and the time comes to apply that credit, simply click on 'Receive Payment' for that invoice and you will have have the option to select the credit. Simply tick the invoice and the credit and these will match together :)
Let me know if there is anything else I can help with and I will be back touch.