Thanks for getting back to me ZNP12 - you wouldn't have to create the employee as a customer for this. To record the repayments, you can create a bank deposit (+ New > Bank deposit) with the bank account that the deducted pay is sent to under 'account', the date the repayment was made, and then scroll to 'add funds to this deposit'.
From here, set the 'VAT amounts' drop-down to 'No VAT'. Under 'received from' select the employee, under 'account' select the same account used on the paid invoice (if you're unsure which account to use here, we'd recommend reaching out to your bookkeeper or accountant), complete the other fields as you see fit and enter the repayment amount. Once saved, you'll see the balance of the account used reduced, and once all repayments have been recorded the net impact will be 0.00.
Although the transactions aren't linked, you can copy the URL of the saved transaction and then open and paste this into the 'memo' of the bill (invoice) for reference.
If you're using QuickBooks Online Plus or Advanced, a quicker way to do this would be using billable expenses. Simply tick the billable field on the bill (the paid invoice) and click the customer/project field to select your employee (you can select + New to create them as a customer if they don't appear here). To enter the repayments, create an invoice with the customer selected - this will autofill with the details of the billable expense, where you can edit the amount field.
