Hello,
If "Lead Status Only" is checked when you enter a new Lead that means that Customer (Lead) entry wouldn't go over to QuickBooks unless a transaction is performed (sent to QuickBooks) or the checkbox is manually unchecked.
Any transaction be it Estimate, Invoice, etc performed in Method will go over to QuickBooks in real time for that Customer provided that the 'Wait for Sync Approval?' is unchecked, if it is checked then it will go over to QuickBooks once it is approved.