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.
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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.
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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.