If you don't see a match to the transactions when selecting 'find match' on your bank screen, you can instead record the payments against the invoice manually.
To do this, open the invoice and select 'Receive payment' - on the following screen, select the payment date, the account that the money was received to (under 'deposit to'), and edit the 'amount received' to the partial amount. Select save & new to record the second partial payment. After saving, you can then match these to the payments on your connected bank feed.
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