Customer Paid Invoice Twice

Good Morning Barry,

The second payment can be entered as credit for the customer by inputting the payment through Sales > Money In. This allows the money to float until it is allocated at a later date.

When you are ready to use the floating funds go to Money > Unallocated Cash. Here you can allocate the funds to a future invoice.

Thanks, Theo

Edit: In addition to what I outlined above, a similar process can be done via imported bank statements. You initially need to head to Settings > Accounting > Account Codes, from here you need to enable "Trade Debtors" to be shown in sales.

After completing this step, it allows for the credit amount from the second invoice to be placed in an account (Trade Debtors) that allows it to be allocated at a future date. Again via the Money > Unallocated Cash section.