I'm here to help share some clarifications about converting invoices from Sage into QuickBooks Desktop.
In situations like this, you'll need to make sure that the payments are linked properly to your invoices. Once verified that payments were detached from the invoice, you may reapply it by following these steps:
Open the invoice that the payment should not have been applied to.
Go to the Reports tab and click Transaction History.
On the Transaction history window, select the payment and click Go To.
On the Customer Payment window, remove the check-mark from the invoice that the payment should not have been applied to.
Put a check mark on the invoice(s) that the payment should be applied to.
Select Save & New.
This will apply the payment to the invoice(s) you selected and remove it from the original invoice it was applied to.