Service Fusion has two kinds of payments: Job Deposits and Invoice Payments.
A Job Deposit is received prior to the job being completed and invoiced.
An Invoice Payment is received after the job is invoiced.
Both types of payments will sync to QuickBooks, however, because a Job Deposit is received before an invoice is created, it will not apply to invoices in QuickBooks, but will instead sit as an unapplied payment. Yes, even after the invoice has been created and synced! However, Service Fusion allows the conversion of Job Deposits to Invoice Payments, which prompts the payment to re-sync and apply to the invoice in QuickBooks Online. Please note: with QuickBooks Desktop, when you convert the job deposit to an invoice payment, you will need to manually apply the deposit to the appropriate invoice in QuickBooks, as it will not be able to automatically apply it.
How do you convert a Job Deposit to an Invoice Payment? First, you'll need to find the Job Deposit in question. You can find your Job Deposit by going to Accounting > View Job Deposits and clicking View on the payment.
Alternatively, you can go to your payment from the View Invoice screen, by clicking the payment amount on the bottom right corner (blue link) then clicking the payment date on the pop-up, to navigate to the View Payment screen.
In the top right corner of the View Deposit screen is the Convert to Invoice Payment button.
Simply click the Convert To Invoice Payment button and the Job Deposit will convert to an Invoice Payment. If you use QuickBooks Online, you may be prompted to resync the payment, or it may auto-sync, depending on your settings. If you use QuickBooks Desktop, the payment will need to be manually applied to the invoice in QuickBooks Desktop. Once that has been updated, either by resyncing (QBO) or manually applying it (QBD) the payment will no longer be sitting on the account as an unapplied payment.