Before learning how to sync invoices, let's make sure our settings within the service box are correct. So go to your settings tab> invoices> statuses.
Statuses- This will display list of status you have for your invoice category, each status functions as per the settings set on this page. Each invoice is synced over to QuickBooks Online based on the status .
If the invoice is in 'Submitted' or 'PAID' status it will sync over to your QuickBooks Online because on this page it has been set to 'YES' under 'Export to Accounting'. However, invoices in 'Draft' and 'Cancelled' status will not be synced because they have been set to 'NO' UNDER ' Export to Accounting' on this page.
Same is for PAID- Software will mark invoice as PAID once the payment is received either in QuickBooks Online or in Service Box. We recommend to set Paid to Yes for at least one status.
Now when you have set your settings for invoice status within service box, next step would be to perform the sync.
Invoice sync without payment : Let's say you have invoice within ServiceBox without payment and you would like to sync it to QuickBooks Online. First check your invoice is in right status. 
Then go to your login name on the top right corner and click on the drop down menu and navigate to QuickBooks Online and click on 'GO' 
Look for that invoice in your QuickBooks Online and you will see that it will indicate that the payment has to be received yet.
Once the payment is received in your QuickBooks Online, run the sync again and software will auto-mark that invoice status as "PAID" 
Invoice Sync with Payment: Let's say, the payment has been received within service box for a invoice and we have to sync that invoice over to QuickBooks Online.
Let's check the invoice is in right status i.e. ' PAID' 
Then go to your login name on the top right corner and click on the drop down menu and navigate to QuickBooks Online and click on 'GO'
Look for that invoice in your QuickBooks Online and you will see that it will indicate that the payment has been received.
Invoice sync with Refund : If the payment is received within Service box you can give refund within the invoice and reflect that change in QuickBooks Online as well.
-Edit the invoice on which you want to add the refund amount ( unlink it if that invoice has already been linked with QuickBooks Online)
-Go to the payments tab on the invoice> edit the payment line item and add the refund amount and click ok. 
- Run the sync again and look for that invoice in your QuickBooks Online, it will indicate the refund amount. 
If the payment has not been received within Service box then you would have to manually do those changes on both the ends.
This should help with your Invoice Sync, if you have any questions please reach out to the support team by sending a message through the feedback button.