Unfortunately you’re not able to break the prepayment down to smaller amounts to use against multiple invoices. However, if the prepayment is greater than the invoice balance, the remaining amount will still be a prepayment.
For example, if you have an invoice for £50, and a pre-payment for £200, paying off the £50 will leave a £150 prepayment balance.
If you then use the remaining £150 against an invoice worth £175, the prepayment will have been used up, but a balance of £25 will remain on the invoice.
I hope that makes sense?
[Edit]
I’ve found this topic which may help in your situation: