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Hello Vrgsy,
If you got to the cog wheel>account and setting>sales>sales form content>turn deposit on> save and then done. Go to the plus and invoice, create the invoice and it has a deposit box which you can put in and this will show as included in the full amount and will show the rest as balance due, so when they have paid it you and click receive payment for the rest of the amount that is due to be paid.
Within the invoice you can allocate the deposit proportion you received to the bank account that it was received to.
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