Great! You have received money to your bank account so it's a time to start keeping track which invoices are paid. You can mark invoices paid from the invoice list or by opening an invoice separately. You can mark an invoice paid or partly paid. If you got only partly paid, you'll have to insert the sum manually into the "Paid total" field.
Click the symbol at the end of the row in the Sales invoices list
Or open the invoice and click Payments:
Can I send a a reminder for a partly paid invoice?
Yes, you can. The invoice will show the amount that is still left to be paid, taking into account the possible payments you have added to the invoice.
Can I create a credit note to a partly paid invoice?
If the invoice is partly paid, you can't create a credit note to it. You can only create a credit note to the whole sum of an invoice. Unpaid receivables can be written off as unpaid.